@article{emanuelson_ankenbruck_kumbhare_thomas_connelly_baktash_randall_deiters_2022, title={Transcriptional Inhibition of MicroRNA miR-122 by Small Molecules Reduces Hepatitis C Virus Replication in Liver Cells}, ISSN={["1520-4804"]}, DOI={10.1021/acs.jmedchem.2c01141}, abstractNote={MicroRNAs (miRNAs) are noncoding RNA molecules of 22-24 nucleotides that are estimated to regulate thousands of genes in humans, and their dysregulation has been implicated in many diseases. MicroRNA-122 (miR-122) is the most abundant miRNA in the liver and has been linked to the development of hepatocellular carcinoma and hepatitis C virus (HCV) infection. Its role in these diseases renders miR-122 a potential target for small-molecule therapeutics. Here, we report the discovery of a new sulfonamide class of small-molecule miR-122 inhibitors from a high-throughput screen using a luciferase-based reporter assay. Structure-activity relationship (SAR) studies and secondary assays led to the development of potent and selective miR-122 inhibitors. Preliminary mechanism-of-action studies suggest a role in the promoter-specific transcriptional inhibition of miR-122 expression through direct binding to the liver-enriched transcription factor hepatocyte nuclear factor 4α. Importantly, the developed inhibitors significantly reduce HCV replication in human liver cells.}, journal={JOURNAL OF MEDICINAL CHEMISTRY}, author={Emanuelson, Cole and Ankenbruck, Nicholas and Kumbhare, Rohan and Thomas, Meryl and Connelly, Colleen and Baktash, Yasmine and Randall, Glenn and Deiters, Alexander}, year={2022}, month={Nov} }
 @article{rahman_zhou_deiters_haugh_2020, title={Optical control of MAP kinase kinase 6 (MKK6) reveals that it has divergent roles in pro-apoptotic and anti-proliferative signaling}, volume={295}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.RA119.012079}, abstractNote={The selective pressure imposed by extrinsic death signals and stressors adds to the challenge of isolating and interpreting the roles of proteins in stress-activated signaling networks. By expressing a kinase with activating mutations and a caged lysine blocking the active site, we can rapidly switch on catalytic activity with light and monitor the ensuing dynamics. Applying this approach to MAP kinase 6 (MKK6), which activates the p38 subfamily of MAPKs, we found that decaging active MKK6 in fibroblasts is sufficient to trigger apoptosis in a p38-dependent manner. Both in fibroblasts and in a murine melanoma cell line expressing mutant B-Raf, MKK6 activation rapidly and potently inhibited the pro-proliferative extracellular signal–regulated kinase (ERK) pathway; to our surprise, this negative cross-regulation was equally robust when all p38 isoforms were inhibited. These results position MKK6 as a new pleiotropic signal transducer that promotes both pro-apoptotic and anti-proliferative signaling, and they highlight the utility of caged, light-activated kinases for dissecting stress-activated signaling networks. The selective pressure imposed by extrinsic death signals and stressors adds to the challenge of isolating and interpreting the roles of proteins in stress-activated signaling networks. By expressing a kinase with activating mutations and a caged lysine blocking the active site, we can rapidly switch on catalytic activity with light and monitor the ensuing dynamics. Applying this approach to MAP kinase 6 (MKK6), which activates the p38 subfamily of MAPKs, we found that decaging active MKK6 in fibroblasts is sufficient to trigger apoptosis in a p38-dependent manner. Both in fibroblasts and in a murine melanoma cell line expressing mutant B-Raf, MKK6 activation rapidly and potently inhibited the pro-proliferative extracellular signal–regulated kinase (ERK) pathway; to our surprise, this negative cross-regulation was equally robust when all p38 isoforms were inhibited. These results position MKK6 as a new pleiotropic signal transducer that promotes both pro-apoptotic and anti-proliferative signaling, and they highlight the utility of caged, light-activated kinases for dissecting stress-activated signaling networks. Cells respond to their dynamically changing and chemically diverse surroundings through highly regulated, intracellular signal transduction networks. Some cellular responses, such as growth and cell cycle progression, may be viewed as short-term, whereas responses such as terminal differentiation and programmed cell death (apoptosis) may be viewed as decisive and cell fate-determining, with limited or no plasticity. Core modules in signal transduction networks include the mitogen-activated protein kinase (MAPK) cascades, notably the extracellular signal–regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38 pathways in mammals (1Chang L. Karin M. Mammalian MAP kinase signalling cascades.Nature. 2001; 410 (11242034): 37-4010.1038/35065000Crossref PubMed Scopus (4170) Google Scholar, 2Johnson G.L. Lapadat R. Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases.Science. 2002; 298 (12471242): 1911-191210.1126/science.1072682Crossref PubMed Scopus (3240) Google Scholar). 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MKK6 activation also rapidly induces potent inhibition of the ERK pathway; surprisingly, we discovered that this negative cross-talk is essentially p38-independent. This finding was replicated in a murine melanoma line with mutant B-Raf, and optical triggering of MKK6 in these oncogene-addicted cells abrogated ERK-dependent cell division. These results position MKK6 as a pleiotropic signal transducer that both promotes cell death and inhibits pro-proliferative signaling, and they demonstrate the utility of caged kinases as unique tools for dissecting signaling networks—stress-activated pathways in particular. To parse the functions of a stress-activated signaling pathway in cells, we developed a genetically encoded, optically controlled MKK6. The incorporation of the caged lysine (CK) (Fig. 1A) through site-directed, unnatural amino acid mutagenesis has enabled the development of light-activatable proteins. This approach utilizes an orthogonal aminoacyl-tRNA synthetase/tRNA pair to selectively incorporate an unnatural amino acid (UAA) into proteins, in response to a recoded UAG amber codon, introduced at a desired site into a gene of interest. Supplementing the protein biosynthetic machinery of cells and animals with an engineered Methanosarcina barkeri pyrrolysyl-tRNA synthetase (pylRS) and its cognate tRNACUA (pylT) enables the incorporation of a wide range of UAAs, including photocaged amino acids (36Courtney T. Deiters A. Recent advances in the optical control of protein function through genetic code expansion.Curr. Opin. Chem. Biol. 2018; 46 (30056281): 99-10710.1016/j.cbpa.2018.07.011Crossref PubMed Scopus (40) Google Scholar). Photocaged amino acids, such as the CK (31Gautier A. Nguyen D.P. Lusic H. An W. Deiters A. Chin J.W. Genetically encoded photocontrol of protein localization in mammalian cells.J. Am. Chem. Soc. 2010; 132 (20218600): 4086-408810.1021/ja910688sCrossref PubMed Scopus (170) Google Scholar), contain a light-removable protecting group that imposes steric demand on an enzyme active site and alters the electronic and nucleophilic characteristics of amino acid side chains. This renders the protein of interest inactive until a brief light exposure (e.g. 365-nm irradiation) removes the caging group and generates the protein's WT catalytic site. This is a generalizable approach for the study of protein kinases (32Gautier A. Deiters A. Chin J.W. Light-activated kinases enable temporal dissection of signaling networks in living cells.J. Am. Chem. Soc. 2011; 133 (21271704): 2124-212710.1021/ja1109979Crossref PubMed Scopus (112) Google Scholar, 40Liaunardy-Jopeace A. Murton B.L. Mahesh M. Chin J.W. James J.R. Encoding optical control in LCK kinase to quantitatively investigate its activity in live cells.Nat. Struct. Mol. 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High-sensitivity measurements of multiple kinase activities in live single cells.Cell. 2014; 157 (24949979): 1724-173410.1016/j.cell.2014.04.039Abstract Full Text Full Text PDF PubMed Scopus (223) Google Scholar), and the transfected cells were supplemented with or without CK (2 mm). After washing the cells and replacing the medium with imaging buffer, reporter localization was monitored by live-cell epifluorescence microscopy. In cells expressing caged MKK6 and incubated with CK, a brief (<2-s) exposure to UV light (DAPI excitation filter) rapidly induced p38 kinase activity, as shown by the live-cell reporter (45Regot S. Hughey J.J. Bajar B.T. Carrasco S. Covert M.W. High-sensitivity measurements of multiple kinase activities in live single cells.Cell. 2014; 157 (24949979): 1724-173410.1016/j.cell.2014.04.039Abstract Full Text Full Text PDF PubMed Scopus (223) Google Scholar) (Fig. 2, B and C), confirming that MKK6 photoactivation and activation of p38 (the canonical MKK6 substrate) was substantial. No such UV-induced translocation responses were observed in the negative controls: cells incubated without CK (Fig. 2C) or in cells incubated with CK but expressing mCherry in place of constitutively active MKK6 (Fig. S1, A–C). These controls indicate that p38 is not activated by a brief UV exposure alone or by decaging of lysines that might have been incorporated in an inert protein or the endogenous proteome. The translocation response in caged MKK6-expressing cells was promptly and completely reversed following the addition of the p38α/β-specific inhibitor SB 239063 (46Underwood D.C. Osborn R.R. Kotzer C.J. Adams J.L. Lee J.C. Webb E.F. Carpenter D.C. Bochnowicz S. Thomas H.C. Hay D.W.P. Griswold D.E. SB 239063, a potent p38 MAP kinase inhibitor, reduces inflammatory cytokine production, airways eosinophil infiltration, and persistence.J. Pharmacol. Exp. Ther. 2000; 293 (10734180): 281-288PubMed Google Scholar) (10 μm; Fig. 2D). The extent and kinetics of the p38 reporter response elicited by MKK6 decaging were comparable with those elicited by the chemical stressor, anisomycin (Fig. 2E). We also confirmed that brief UV exposure does not induce significant translocation of the analogous JNK activity reporter, either with or without expression of caged MKK6 (Fig. 2F and Fig. S1D). For Fig. 2 (C–F), variability among the time courses of the individual cells is shown in Fig. S2. Taken together, these results establish an experimental system in which canonical MKK6 → p38 signaling is readily and specifically induced by a brief and benign exposure to low-energy UV light. 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To quantify apoptotic responses more precisely, we monitored the release of fluorescent protein-tagged cytochrome c from mitochondria, a hallmark of apoptosis (54Goldstein J.C. Waterhouse N.J. Juin P. Evan G.I. Green D.R. The coordinate release of cytochrome c during apoptosis is rapid, complete and kinetically invariant.Nat. Cell Biol. 2000; 2 (10707086): 156-16210.1038/35004029Crossref PubMed Scopus (840) Google Scholar, 55Chen Q. Gong B. Almasan A. Distinct stages of cytochrome c release from mitoch}, number={25}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Rahman, Shah Md. Toufiqur and Zhou, Wenyuan and Deiters, Alexander and Haugh, Jason M.}, year={2020}, month={Jun}, pages={8494–8504} }
 @article{enamorado_connelly_deiters_comins_2015, title={A concise synthesis of the Lycopodium alkaloid cermizine D}, volume={56}, ISSN={["0040-4039"]}, DOI={10.1016/j.tetlet.2015.04.013}, abstractNote={A racemic and asymmetric synthesis of cermizine D (1) was accomplished in six steps from 4-methoxypyridine or 4-methoxy-3-TIPS-pyridine in 12% and 13% overall yield, respectively. A key step is a stereoselective 1,4-addition of a 2-((trimethylsilyl)methyl)pyridine-derived cuprate to a bicyclic 2,3-dihydro-4-pyridone. Racemic and (−)-cermizine D failed to exhibit cytotoxicity against four different cell lines.}, number={23}, journal={TETRAHEDRON LETTERS}, author={Enamorado, Monica F. and Connelly, Colleen M. and Deiters, Alexander and Comins, Daniel L.}, year={2015}, month={Jun}, pages={3683–3685} }
 @article{hemphill_liu_uprety_samanta_tsang_juliano_deiters_2015, title={Conditional Control of Alternative Splicing through Light-Triggered Splice-Switching Oligonucleotides}, volume={137}, ISSN={["0002-7863"]}, DOI={10.1021/jacs.5b00580}, abstractNote={The spliceosome machinery is composed of several proteins and multiple small RNA molecules that are involved in gene regulation through the removal of introns from pre-mRNAs in order to assemble exon-based mRNA containing protein-coding sequences. Splice-switching oligonucleotides (SSOs) are genetic control elements that can be used to specifically control the expression of genes through correction of aberrant splicing pathways. A current limitation with SSO methodologies is the inability to achieve conditional control of their function paired with high spatial and temporal resolution. We addressed this limitation through site-specific installation of light-removable nucleobase-caging groups as well as photocleavable backbone linkers into synthetic SSOs. This enables optochemical OFF → ON and ON → OFF switching of their activity and thus precise control of alternative splicing. The use of light as a regulatory element allows for tight spatial and temporal control of splice switching in mammalian cells and animals.}, number={10}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Hemphill, James and Liu, Qingyang and Uprety, Rajendra and Samanta, Subhas and Tsang, Michael and Juliano, Rudolph L. and Deiters, Alexander}, year={2015}, month={Mar}, pages={3656–3662} }
 @article{brown_zou_shirvanyants_zhang_samanta_mantravadi_dokholyan_deiters_2015, title={Light-cleavable rapamycin dimer as an optical trigger for protein dimerization}, volume={51}, ISSN={["1364-548X"]}, DOI={10.1039/c4cc09442e}, abstractNote={Protein heterodimerization of FKBP12 and FRB can be optically controlled with a photocleavable rapamycin dimer.}, number={26}, journal={CHEMICAL COMMUNICATIONS}, author={Brown, Kalyn A. and Zou, Yan and Shirvanyants, David and Zhang, Jie and Samanta, Subhas and Mantravadi, Pavan K. and Dokholyan, Nikolay V. and Deiters, Alexander}, year={2015}, pages={5702–5705} }
 @article{govan_young_lively_deiters_2015, title={Optically triggered immune response through photocaged oligonucleotides}, volume={56}, ISSN={["0040-4039"]}, DOI={10.1016/j.tetlet.2015.01.165}, abstractNote={Bacterial and viral CpG oligonculeotides are unmethylated cytosine-phosphate-guanosine dinucleotide sequences and trigger an innate immune response through activation of the toll-like receptor 9 (TLR9). We have developed synthetic photocaged CpGs via site-specific incorporation of nitropiperonyloxymethyl (NPOM)-caged thymidine residues. These oligonucleotides enable the optical control of TLR9 function and thereby provide light-activation of an immune response. We provide a proof-of-concept model by applying a reporter assay in live cells and by quantification of endogenous production of interleukin 6.}, number={23}, journal={TETRAHEDRON LETTERS}, author={Govan, Jeane M. and Young, Douglas D. and Lively, Mark O. and Deiters, Alexander}, year={2015}, month={Jun}, pages={3639–3642} }
 @article{engelke_chou_uprety_jess_deiters_2014, title={Control of Protein Function through Optochemical Translocation}, volume={3}, ISSN={["2161-5063"]}, DOI={10.1021/sb400192a}, abstractNote={Controlled manipulation of proteins and their function is important in almost all biological disciplines. Here, we demonstrate control of protein activity with light. We present two different applications—light-triggered transcription and light-triggered protease cleavage—both based on the same concept of protein mislocation, followed by optochemically triggered translocation to an active cellular compartment. In our approach, we genetically encode a photocaged lysine into the nuclear localization signal (NLS) of the transcription factor SATB1. This blocks nuclear import of the protein until illumination induces caging group removal and release of the protein into the nucleus. In the first application, prepending this NLS to the transcription factor FOXO3 allows us to optochemically switch on its transcription activity. The second application uses the developed light-activated NLS to control nuclear import of TEV protease and subsequent cleavage of nuclear proteins containing TEV cleavage sites. The small size of the light-controlled NLS (only 20 amino acids) minimizes impact of its insertion on protein function and promises a general approach to a wide range of optochemical applications. Since the light-activated NLS is genetically encoded and optically triggered, it will prove useful to address a variety of problems requiring spatial and temporal control of protein function, for example, in stem-cell, developmental, and cancer biology.}, number={10}, journal={ACS SYNTHETIC BIOLOGY}, author={Engelke, Hanna and Chou, Chungjung and Uprety, Rajendra and Jess, Phillip and Deiters, Alexander}, year={2014}, month={Oct}, pages={731–736} }
 @article{uprety_luo_liu_naro_samanta_deiters_2014, title={Genetic Encoding of Caged Cysteine and Caged Homocysteine in Bacterial and Mammalian Cells}, volume={15}, ISSN={["1439-7633"]}, DOI={10.1002/cbic.201400073}, abstractNote={We report the genetic incorporation of caged cysteine and caged homocysteine into proteins in bacterial and mammalian cells. The genetic code of these cells was expanded with an engineered pyrrolysine tRNA/tRNA synthetase pair that accepts both light-activatable amino acids as substrates. Incorporation was validated by reporter assays, western blots, and mass spectrometry, and differences in incorporation efficiency were explained by molecular modeling of synthetase–amino acid interactions. As a proof-of-principle application, the genetic replacement of an active-site cysteine residue with a caged cysteine residue in Renilla luciferase led to a complete loss of enzyme activity; however, upon brief exposure to UV light, a >150-fold increase in enzymatic activity was observed, thus showcasing the applicability of the caged cysteine in live human cells. A simultaneously conducted genetic replacement with homocysteine yielded an enzyme with greatly reduced activity, thereby demonstrating the precise probing of a protein active site. These discoveries provide a new tool for the optochemical control of protein function in mammalian cells and expand the set of genetically encoded unnatural amino acids.}, number={12}, journal={CHEMBIOCHEM}, author={Uprety, Rajendra and Luo, Ji and Liu, Jihe and Naro, Yuta and Samanta, Subhas and Deiters, Alexander}, year={2014}, month={Aug}, pages={1793–1799} }
 @article{lee_kurra_yang_torres-kolbus_deiters_liu_2014, title={Genetically encoded unstrained olefins for live cell labeling with tetrazine dyes}, volume={50}, ISSN={["1364-548X"]}, DOI={10.1039/c4cc06435f}, abstractNote={A number of non-canonical amino acids (NCAAs) with unstrained olefins are genetically encoded using mutant pyrrolysyl-tRNA synthetase–tRNAPylCUA pairs for catalyst-free labeling with tetrazine dyes.}, number={86}, journal={CHEMICAL COMMUNICATIONS}, author={Lee, Yan-Jiun and Kurra, Yadagiri and Yang, Yanyan and Torres-Kolbus, Jessica and Deiters, Alexander and Liu, Wenshe R.}, year={2014}, pages={13085–13088} }
 @article{lee_kurra_yang_torres-kolbus_deiters_liu_2014, title={Genetically encoded unstrained olefins for live cell labeling with tetrazine dyes (vol 50, pg 13085, 2014)}, volume={50}, ISSN={["1364-548X"]}, DOI={10.1039/c4cc90401j}, abstractNote={Correction for ‘Genetically encoded unstrained olefins for live cell labeling with tetrazine dyes’ by Yan-Jiun Lee et al., Chem. Commun., 2014, DOI: 10.1039/c4cc06435f.}, number={87}, journal={CHEMICAL COMMUNICATIONS}, author={Lee, Yan-Jiun and Kurra, Yadagiri and Yang, Yanyan and Torres-Kolbus, Jessica and Deiters, Alexander and Liu, Wenshe R.}, year={2014}, month={Nov}, pages={13396–13396} }
 @article{walsh_gardner_deiters_williams_2014, title={Intracellular Light-Activation of Riboswitch Activity}, volume={15}, ISSN={1439-4227}, url={http://dx.doi.org/10.1002/cbic.201400024}, DOI={10.1002/cbic.201400024}, abstractNote={By combining a riboswitch with a cell-permeable photocaged small-molecule ligand, an optochemical gene control element was constructed that enabled spatial and temporal control of gene expression in bacterial cells. The simplicity of this strategy, coupled with the ability to create synthetic riboswitches with tailored ligand specificities and output in a variety of microorganisms, plants, and fungi might afford a general strategy to photocontrol gene expression in vivo. The ability to activate riboswitches by using light enables the interrogation and manipulation of a wide range of biological processes with high precision, and will have broad utility in the regulation of artificial genetic circuits.}, number={9}, journal={ChemBioChem}, publisher={Wiley}, author={Walsh, Steven and Gardner, Laura and Deiters, Alexander and Williams, Gavin J.}, year={2014}, month={May}, pages={1346–1351} }
 @article{volvert_prevot_close_laguesse_pirotte_hemphill_rogister_kruzy_sacheli_moonen_et al._2014, title={MicroRNA Targeting of CoREST Controls Polarization of Migrating Cortical Neurons}, volume={7}, ISSN={["2211-1247"]}, DOI={10.1016/j.celrep.2014.03.075}, abstractNote={•MicroRNAs control radial migration through regulation of cortical neuron polarization•miR-22 and miR-124 are critical regulators of neuron morphology during migration•miR-22 and miR-124 target the CoREST/REST complex to fine-tune doublecortin expression The migration of cortical projection neurons is a multistep process characterized by dynamic cell shape remodeling. The molecular basis of these changes remains elusive, and the present work describes how microRNAs (miRNAs) control neuronal polarization during radial migration. We show that miR-22 and miR-124 are expressed in the cortical wall where they target components of the CoREST/REST transcriptional repressor complex, thereby regulating doublecortin transcription in migrating neurons. This molecular pathway underlies radial migration by promoting dynamic multipolar-bipolar cell conversion at early phases of migration, and later stabilization of cell polarity to support locomotion on radial glia fibers. Thus, our work emphasizes key roles of some miRNAs that control radial migration during cerebral corticogenesis. The migration of cortical projection neurons is a multistep process characterized by dynamic cell shape remodeling. The molecular basis of these changes remains elusive, and the present work describes how microRNAs (miRNAs) control neuronal polarization during radial migration. We show that miR-22 and miR-124 are expressed in the cortical wall where they target components of the CoREST/REST transcriptional repressor complex, thereby regulating doublecortin transcription in migrating neurons. This molecular pathway underlies radial migration by promoting dynamic multipolar-bipolar cell conversion at early phases of migration, and later stabilization of cell polarity to support locomotion on radial glia fibers. Thus, our work emphasizes key roles of some miRNAs that control radial migration during cerebral corticogenesis. The cerebral cortex comprises six layers of neurons born in the progenitor zones of the forebrain. Dorsal cortical progenitors generate temporal cohorts of neurons that undergo active migration to reach their final positions in successive cortical layers where they extend neurites to finalise contacts with target cells (Bielas et al., 2004Bielas S. Higginbotham H. Koizumi H. Tanaka T. Gleeson J.G. 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Cuellar T.L. Koch S.M. Barker A.J. Harfe B.D. McManus M.T. Ullian E.M. Conditional loss of Dicer disrupts cellular and tissue morphogenesis in the cortex and hippocampus.J. Neurosci. 2008; 28: 4322-4330Crossref PubMed Scopus (369) Google Scholar, De Pietri Tonelli et al., 2008De Pietri Tonelli D. Pulvers J.N. Haffner C. Murchison E.P. Hannon G.J. Huttner W.B. miRNAs are essential for survival and differentiation of newborn neurons but not for expansion of neural progenitors during early neurogenesis in the mouse embryonic neocortex.Development. 2008; 135: 3911-3921Crossref PubMed Scopus (288) Google Scholar, Kawase-Koga et al., 2009Kawase-Koga Y. Otaegi G. Sun T. Different timings of Dicer deletion affect neurogenesis and gliogenesis in the developing mouse central nervous system.Dev. Dyn. 2009; 238: 2800-2812Crossref PubMed Scopus (205) Google Scholar, Makeyev et al., 2007Makeyev E.V. Zhang J. Carrasco M.A. Maniatis T. The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing.Mol. Cell. 2007; 27: 435-448Abstract Full Text Full Text PDF PubMed Scopus (1064) Google Scholar, Nowakowski et al., 2011Nowakowski T.J. Mysiak K.S. Pratt T. Price D.J. Functional dicer is necessary for appropriate specification of radial glia during early development of mouse telencephalon.PLoS ONE. 2011; 6: e23013Crossref PubMed Scopus (46) Google Scholar). Although cortical phenotypes resulted from loss of mature miRNAs, functional connections to individual miRNA have been mostly correlative. In addition, miRNA modulations were performed in progenitors, which may have secondary impact on the mobility of projection neurons (Clovis et al., 2012Clovis Y.M. Enard W. Marinaro F. Huttner W.B. De Pietri Tonelli D. Convergent repression of Foxp2 3’UTR by miR-9 and miR-132 in embryonic mouse neocortex: implications for radial migration of neurons.Development. 2012; 139: 3332-3342Crossref PubMed Scopus (109) Google Scholar, Gaughwin et al., 2011Gaughwin P. Ciesla M. Yang H. Lim B. Brundin P. Stage-specific modulation of cortical neuronal development by Mmu-miR-134.Cereb. Cortex. 2011; 21: 1857-1869Crossref PubMed Scopus (124) Google Scholar, Kawase-Koga et al., 2009Kawase-Koga Y. Otaegi G. Sun T. Different timings of Dicer deletion affect neurogenesis and gliogenesis in the developing mouse central nervous system.Dev. Dyn. 2009; 238: 2800-2812Crossref PubMed Scopus (205) Google Scholar, Sun et al., 2011Sun G. Ye P. Murai K. Lang M.F. Li S. Zhang H. Li W. Fu C. Yin J. Wang A. et al.miR-137 forms a regulatory loop with nuclear receptor TLX and LSD1 in neural stem cells.Nat. Commun. 2011; 2: 529Crossref PubMed Scopus (222) Google Scholar). Therefore, there is currently no evidence that miRNAs directly control the migration of postmitotic projection neurons (Volvert et al., 2012Volvert M.L. Rogister F. Moonen G. Malgrange B. Nguyen L. MicroRNAs tune cerebral cortical neurogenesis.Cell Death Differ. 2012; 19: 1573-1581Crossref PubMed Scopus (53) Google Scholar). By combining microarray analyses with conditional deletion of Dicer in newborn projection neurons and time-lapse recording on organotypic brain slices, we identified two miRNAs that control neuronal migration in the developing cortex. Indeed, we showed that, by targeting elements of the CoREST/REST transcriptional repressor complex, miR-22 and miR-124 control the expression of Doublecortin (Dcx), a microtubule-associated protein (MAP) that contributes to the establishment of neuron polarization and radial migration in the cerebral cortex. Disruption of Dicer in cortical progenitors from Dicerlox/lox;FOXG1Cre/+ embryos (Cobb et al., 2005Cobb B.S. Nesterova T.B. Thompson E. Hertweck A. O’Connor E. Godwin J. Wilson C.B. Brockdorff N. Fisher A.G. Smale S.T. Merkenschlager M. T cell lineage choice and differentiation in the absence of the RNase III enzyme Dicer.J. Exp. Med. 2005; 201: 1367-1373Crossref PubMed Scopus (432) Google Scholar, Hébert and McConnell, 2000Hébert J.M. McConnell S.K. Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures.Dev. Biol. 2000; 222: 296-306Crossref PubMed Scopus (429) Google Scholar) resulted in major corticogenesis defects (Figures S1A–S1E), as reported previously (Volvert et al., 2012Volvert M.L. Rogister F. Moonen G. Malgrange B. Nguyen L. MicroRNAs tune cerebral cortical neurogenesis.Cell Death Differ. 2012; 19: 1573-1581Crossref PubMed Scopus (53) Google Scholar). Although projection neurons were misplaced (Figure S1D) in the cortical wall, we could not decipher whether Dicer cell autonomously controlled neuronal migration because loss of glial scaffold integrity (Figure S1C), poor cell survival, proliferation, and specification defects (Figures S1B and S1E) secondarily alter radial migration. Therefore, we analyzed embryos that lacked Dicer specifically in postmitotic projection neurons. This was achieved by breeding Dicerlox/lox with NEXCre/+ (Goebbels et al., 2006Goebbels S. Bormuth I. Bode U. Hermanson O. Schwab M.H. Nave K.A. Genetic targeting of principal neurons in neocortex and hippocampus of NEX-Cre mice.Genesis. 2006; 44: 611-621Crossref PubMed Scopus (334) Google Scholar) (termed hereafter Dicer CKO) mice. We assessed the distribution of Satb2-expressing upper-layer neurons in postnatal (P) 2 wild-type (WT) or Dicer CKO cortices. Although most control neurons settled in layers IV to II, numerous Satb2-postive neurons were misplaced in deep layers of Dicer CKO cortex (Figures 1A–1C). We next performed acute deletion of Dicer in a cohort of embryonic day (E) 14 projection neurons by in utero electroporation (Figure 1D) of plasmids expressing Cre and GFP under a regulatory sequence of NeuroD (NeuroD:Cre-GFP) or only GFP (NeuroD:GFP) (Figures S2A and S2B). Three days after electroporation, NeuroD:Cre-GFP-expressing neurons selected by fluorescent-activated cell sorting (FACS) and further analyzed by quantitative RT-PCR (RT-PCR) had reduced level of Dicer expression, as compared to control (Figure 1E). Acute removal of Dicer at E14 impaired neuronal migration to upper layers (Figures 1F and 1G) without affecting cell survival (data not shown) or integrity of the glial scaffold (Figure S2C). Large amounts of Cre-electroporated projection neurons were still detected in deep layers after birth (Figures 1H and 1I). Most neurons trapped in deep layers expressed the upper-layer markers Satb2 (layers II–IV; Figure 1K) and Cux1 (layers II–IV; Figure S2D) but not the deep-layer marker Sox5 (layers V and VI; Figure 1J), which supports migration defect rather than laminar specification. It is noteworthy that neurons permanently trapped in deep layers harbored unconventional multipolar shapes at P17 (Figures 1L and 1M). Altogether, these results show that Dicer is cell autonomously required for proper migration of projection neurons to upper layers, and they suggest a direct contribution of miRNAs to radial migration. Electroporation of cortical progenitors in E14 Dicerlox/lox embryos led to accumulation of GFP-expressing postmitotic (Ki67 negative) neurons (Tbr2 negative) in the intermediate zone (IZ) 2 days later (Figures 2A and 2B ). A closer look at the cortical wall revealed accumulation of multipolar cells throughout the IZ (Figures 2C and 2D) and the cortical plate (CP), at the expense of bipolar neurons, after acute removal of Dicer (Figures 2E–2G and S2E). These results prompted us to analyze the dynamic conversion of neuron polarity by real-time imaging (Figure 3A). In utero electroporations of NeuroD:Cre-GFP or NeuroD:GFP constructs were performed in E14 Dicerlox/lox embryos that were further harvested at E16 to set up organotypic brain culture. IZ fields were selected, and GFP-positive neurons were recorded the next day for 10 hr. We analyzed the dynamic multipolar-bipolar conversion of cortical neurons (Figure 3A) and showed that the conditional removal of Dicer impaired this process (Figures 3B and 3D; Movie S1). In addition, some bipolar neurons electroporated with NeuroD:Cre-GFP showed unstable polarity, because they could not maintain bipolar shape during the recording (Figures 3C and 3E; Movie S2). Migration to cortical plate further involves a locomotory phase on radial glia fibers (Figures 3A and 3F–3J). When compared to control projection neurons, Cre-electroporated neurons traveled significantly slower (Figure 3G). However, they underwent long pauses, which almost never occurred in control neurons (Figures 3H and 3I). When pauses were substracted from the analysis, the motility index was comparable in both conditions (Figure 3J). Interestingly, pauses were associated with transient loss of cell polarity and most Cre-expressing neurons were indeed multipolar while pausing (Figures 3K and 3L). In addition, Dicer knockout neurons ended migration by shorter somal translocation (Figures S2F–S2I). Altogether, these results demonstrate that Dicer controls the dynamic polarization of newborn cortical neurons to ensure progression through the successive phases of radial migration (Noctor et al., 2004Noctor S.C. Martínez-Cerdeño V. Ivic L. Kriegstein A.R. Cortical neurons arise in symmetric and asymmetric division zones and migrate through specific phases.Nat. Neurosci. 2004; 7: 136-144Crossref PubMed Scopus (1655) Google Scholar).Figure 3Loss of Dicer Results in Morphological Instability during Radial MigrationShow full captionReal-time imaging of NeuroD:GFP or NeuroD:Cre-GFP-expressing Dicerlox/lox neurons at E14 in E16 brain slices cultured for a day. Morphological changes underwent by neurons during radial migration (A). Percentage of multipolar to bipolar cell morphology conversion during 10 hr recording (B), as illustrated by a time-lapse sequence (hr) (D) or the percentage of bipolar morphology maintenance (B), as illustrated by a time-lapse sequence (hr) (E). Locomotory paths (colored dotted lines) of NeuroD:GFP or NeuroD:Cre-GFP electroporated Dicerlox/lox neurons recorded during time lapse imaging (F). Quantification of migration velocity (G), average pause number per 10 hr recording (H), average pause duration (I), or motility index (J) of Dicerlox/lox electroporated neurons at E14 with NeuroD:GFP or NeuroD:Cre-GFP vectors. Percentage of electroporated multipolar cells pausing during locomotion (L), as illustrated by a representative time-lapse sequence (hr). The red dotted line marks the position of a multipolar neuron at standstill during 3 hr, as highlighted by the thick blue line (K). CP, cortical plate; IZ, intermediate zone; VZ, ventricular zone. See also Figure S2 and Movies S1 and S2.View Large Image Figure ViewerDownload (PPT) Real-time imaging of NeuroD:GFP or NeuroD:Cre-GFP-expressing Dicerlox/lox neurons at E14 in E16 brain slices cultured for a day. Morphological changes underwent by neurons during radial migration (A). Percentage of multipolar to bipolar cell morphology conversion during 10 hr recording (B), as illustrated by a time-lapse sequence (hr) (D) or the percentage of bipolar morphology maintenance (B), as illustrated by a time-lapse sequence (hr) (E). Locomotory paths (colored dotted lines) of NeuroD:GFP or NeuroD:Cre-GFP electroporated Dicerlox/lox neurons recorded during time lapse imaging (F). Quantification of migration velocity (G), average pause number per 10 hr recording (H), average pause duration (I), or motility index (J) of Dicerlox/lox electroporated neurons at E14 with NeuroD:GFP or NeuroD:Cre-GFP vectors. Percentage of electroporated multipolar cells pausing during locomotion (L), as illustrated by a representative time-lapse sequence (hr). The red dotted line marks the position of a multipolar neuron at standstill during 3 hr, as highlighted by the thick blue line (K). CP, cortical plate; IZ, intermediate zone; VZ, ventricular zone. See also Figure S2 and Movies S1 and S2. Comparative microarray analyses performed on total RNA extracts from E12 Dicerlox/lox; FoxG1Cre/+ (genetic deletion of Dicer in telencephalic cells) and WT cortices allowed the identification of some differentially expressed genes that control neuronal polarity in the cerebral cortex (Heng et al., 2008Heng J.I. Nguyen L. Castro D.S. Zimmer C. Wildner H. Armant O. Skowronska-Krawczyk D. Bedogni F. Matter J.M. Hevner R. Guillemot F. Neurogenin 2 controls cortical neuron migration through regulation of Rnd2.Nature. 2008; 455: 114-118Crossref PubMed Scopus (220) Google Scholar, LoTurco and Bai, 2006LoTurco J.J. Bai J. The multipolar stage and disruptions in neuronal migration.Trends Neurosci. 2006; 29: 407-413Abstract Full Text Full Text PDF PubMed Scopus (195) Google Scholar, Mandel et al., 2011Mandel G. Fiondella C.G. Covey M.V. Lu D.D. Loturco J.J. Ballas N. Repressor element 1 silencing transcription factor (REST) controls radial migration and temporal neuronal specification during neocortical development.Proc. Natl. Acad. Sci. USA. 2011; 108: 16789-16794Crossref PubMed Scopus (55) Google Scholar). Selected candidates, including FoxP2 (1.92-fold increase in Dicer knockout backround), REST (1.94-fold increase), CoREST (2.11 fold increase), and Rnd2 (2.32-fold decrease), were analyzed by qRT-PCR on RNA extracts from FACS-purified neurons from E17 Dicerlox/lox embryos electroporated in utero with NeuroD:Cre-GFP or NeuroD:GFP at E14. CoREST, a corepressor that associates with the transcriptional repressor REST (Ballas et al., 2005Ballas N. Grunseich C. Lu D.D. Speh J.C. Mandel G. REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis.Cell. 2005; 121: 645-657Abstract Full Text Full Text PDF PubMed Scopus (696) Google Scholar), was the only candidate from our short list (Figures 4A and S3A–S3D) or from published work (stathmin [Westerlund et al., 2011Westerlund N. Zdrojewska J. Padzik A. Komulainen E. Björkblom B. Rannikko E. Tararuk T. Garcia-Frigola C. Sandholm J. Nguyen L. et al.Phosphorylation of SCG10/stathmin-2 determines multipolar stage exit and neuronal migration rate.Nat. Neurosci. 2011; 14: 305-313Crossref PubMed Scopus (91) Google Scholar], neuropilin-1 [Chen et al., 2008Chen G. Sima J. Jin M. Wang K.Y. Xue X.J. Zheng W. Ding Y.Q. Yuan X.B. Semaphorin-3A guides radial migration of cortical neurons during development.Nat. Neurosci. 2008; 11: 36-44Crossref PubMed Scopus (190) Google Scholar], and COUP-TF1 [Alfano et al., 2011Alfano C. Viola L. Heng J.I. Pirozzi M. Clarkson M. Flore G. De Maio A. Schedl A. Guillemot F. Studer M. COUP-TFI promotes radial migration and proper morphology of callosal projection neurons by repressing Rnd2 expression.Development. 2011; 138: 4685-4697Crossref PubMed Scopus (52) Google Scholar]) (Figures S3E–S3H) whose expression was significantly affected. It is noteworthy that the methyl CpG binding protein 2 (MeCP2), an additional component of the CoREST/REST repressor complex, was also slightly increased in Dicer-depleted neurons (Figure S3I). CoREST is indeed a strong candidate because it regulates radial migration (Fuentes et al., 2012Fuentes P. Cánovas J. Berndt F.A. Noctor S.C. Kukuljan M. CoREST/LSD1 control the development of pyramidal cortical neurons.Cereb. Cortex. 2012; 22: 1431-1441Crossref PubMed Scopus (63) Google Scholar), and its protein expression level decreases between E14 and birth in the cortex, when most projection neurons reach their dedicated cortical layer (Figure 4B). These results were further supported the faint detection of CoREST in the IZ, a cortical region enriched in migrating neurons (Figure 4C). It is noteworthy that CoREST expression was heterogenous throughout the CP, with higher expression in early-born Ctip2-expressing neurons that halted migration in deep layers, as compared to upper-layer neurons (Satb2 positives) (Figure 4D). Importantly, coelectroporating NeuroD:Cre-GFP and CoREST small hairpin RNA (shRNA) targeting vectors in Dicerlox/lox neurons normalized CoREST expression to basal level (Figure S3J) and rescued neuronal polarization (Figures 4E and 4F) and migration defects (Figures 4G and 4H) without reducing CoREST expression in cortical progenitors (Figure S3N). On the other hand, in utero expression of CoREST in postmitotic neurons using NeuroD:CoREST vectors impaired their migration in the cortex (Figures S3L and S3M). Altogether, our results sugg}, number={4}, journal={CELL REPORTS}, author={Volvert, Marie-Laure and Prevot, Pierre-Paul and Close, Pierre and Laguesse, Sophie and Pirotte, Sophie and Hemphill, James and Rogister, Florence and Kruzy, Nathalie and Sacheli, Rosalie and Moonen, Gustave and et al.}, year={2014}, month={May}, pages={1168–1183} }
 @misc{liu_deiters_2014, title={Optochemical Control of Deoxyoligonucleotide Function via a Nucleobase-Caging Approach}, volume={47}, ISSN={["1520-4898"]}, DOI={10.1021/ar400036a}, abstractNote={Synthetic oligonucleotides have been extensively applied tocontrol a wide range of biological processes such as gene expression, gene repair, DNA replication, and protein activity. Based on well-established sequence design rules that typically rely on Watson-Crick base pairing interactions researchers can readily program the function of these oligonucleotides. Therefore oligonucleotides provide a flexible platform for targeting a wide range of biological molecules, including DNA, RNA, and proteins. In addition, oligonucleotides are commonly used research tools in cell biology and developmental biology. However, a lack of conditional control methods has hampered the precise spatial and temporal regulation of oligonucleotide activity, which limits the application of these reagents to investigate complex biological questions. Nature controls biological function with a high level of spatial and temporal resolution and in order to elucidate the molecular mechanisms of biological processes, researchers need tools that allow for the perturbation of these processes with Nature's precision. Light represents an excellent external regulatory element since irradiation can be easily controlled spatially and temporally. Thus, researchers have developed several different methods to conditionally control oligonucleotide activity with light. One of the most versatile strategies is optochemical regulation through the installation and removal of photolabile caging groups on oligonucleotides. To produce switches that can control nucleic acid function with light, chemists introduce caging groups into the oligomer backbone or on specific nucleobases to block oligonucleotide function until the caging groups are removed by light exposure. In this Account, we focus on the application of caged nucleobases to the photoregulation of DNA function. Using this approach, we have both activated and deactivated gene expression optochemically at the transcriptional and translational level with spatial and temporal control. Specifically, we have used caged triplex-forming oligomers and DNA decoys to regulate transcription, and we have regulated translation with light-activated antisense agents. Moreover, we also discuss strategies that can trigger DNA enzymatic activity, DNA amplification, and DNA mutagenesis by light illumination. More recently, we have developed light-activated DNA logic operations, an advance that may lay the foundation for the optochemical control of complex DNA calculations.}, number={1}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Liu, Qingyang and Deiters, Alexander}, year={2014}, month={Jan}, pages={45–55} }
 @article{hemphill_govan_uprety_tsang_deiters_2014, title={Site-Specific Promoter Caging Enables Optochemical Gene Activation in Cells and Animals}, volume={136}, ISSN={["1520-5126"]}, DOI={10.1021/ja500327g}, abstractNote={In cell and molecular biology, double-stranded circular DNA constructs, known as plasmids, are extensively used to express a gene of interest. These gene expression systems rely on a specific promoter region to drive the transcription of genes either constitutively (i.e., in a continually “ON” state) or conditionally (i.e., in response to a specific transcription initiator). However, controlling plasmid-based expression with high spatial and temporal resolution in cellular environments and in multicellular organisms remains challenging. To overcome this limitation, we have site-specifically installed nucleobase-caging groups within a plasmid promoter region to enable optochemical control of transcription and, thus, gene expression, via photolysis of the caging groups. Through the light-responsive modification of plasmid-based gene expression systems, we have demonstrated optochemical activation of an exogenous fluorescent reporter gene in both tissue culture and a live animal model, as well as light-induced overexpression of an endogenous signaling protein.}, number={19}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Hemphill, James and Govan, Jeane and Uprety, Rajendra and Tsang, Michael and Deiters, Alexander}, year={2014}, month={May}, pages={7152–7158} }
 @article{torres-kolbus_chou_liu_deiters_2014, title={Synthesis of Non-linear Protein Dimers through a Genetically Encoded Thiol-ene Reaction}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0105467}, abstractNote={Site-specific incorporation of bioorthogonal unnatural amino acids into proteins provides a useful tool for the installation of specific functionalities that will allow for the labeling of proteins with virtually any probe. We demonstrate the genetic encoding of a set of alkene lysines using the orthogonal PylRS/PylTCUA pair in Escherichia coli. The installed double bond functionality was then applied in a photoinitiated thiol-ene reaction of the protein with a fluorescent thiol-bearing probe, as well as a cysteine residue of a second protein, showing the applicability of this approach in the formation of heterogeneous non-linear fused proteins.}, number={9}, journal={PLOS ONE}, author={Torres-Kolbus, Jessica and Chou, Chungjung and Liu, Jihe and Deiters, Alexander}, year={2014}, month={Sep} }
 @article{vonlanthen_connelly_deiters_linden_finney_2014, title={Thiourea-Based Fluorescent Chemosensors for Aqueous Metal Ion Detection and Cellular Imaging}, volume={79}, ISSN={["1520-6904"]}, DOI={10.1021/jo500710g}, abstractNote={We describe three significant advances in the use of thioureas as reporting elements for metal-responsive fluorescent chemosensors. First, on the basis of the crystal structure of a chemosensor analogue, we provide a deeper understanding of the details of the thiourea coordination environment. Second, we describe a new generation of chemosensors with higher affinities for Zn2+ and Cd2+ than were observed for earlier probes, expanding the scope of this type of probe beyond Hg2+ detection. Third, we show that a thiourea-based chemosensor can be employed for fluorescence microscopy imaging of Hg2+ ion concentrations in living mammalian cells.}, number={13}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Vonlanthen, Mireille and Connelly, Colleen M. and Deiters, Alexander and Linden, Anthony and Finney, Nathaniel S.}, year={2014}, month={Jul}, pages={6054–6060} }
 @article{kurra_odoi_lee_yang_lu_wheeler_torres-kolbus_deiters_liu_2014, title={Two Rapid Catalyst-Free Click Reactions for In Vivo Protein Labeling of Genetically Encoded Strained Alkene/Alkyne Functionalities}, volume={25}, ISSN={["1043-1802"]}, DOI={10.1021/bc500361d}, abstractNote={Detailed kinetic analyses of inverse electron-demand Diels–Alder cycloaddition and nitrilimine-alkene/alkyne 1,3-diploar cycloaddition reactions were conducted and the reactions were applied for rapid protein bioconjugation. When reacted with a tetrazine or a diaryl nitrilimine, strained alkene/alkyne entities including norbornene, trans-cyclooctene, and cyclooctyne displayed rapid kinetics. To apply these “click” reactions for site-specific protein labeling, five tyrosine derivatives that contain a norbornene, trans-cyclooctene, or cyclooctyne entity were genetically encoded into proteins in Escherichia coli using an engineered pyrrolysyl-tRNA synthetase-tRNACUAPyl pair. Proteins bearing these noncanonical amino acids were successively labeled with a fluorescein tetrazine dye and a diaryl nitrilimine both in vitro and in living cells.}, number={9}, journal={BIOCONJUGATE CHEMISTRY}, author={Kurra, Yadagiri and Odoi, Keturah A. and Lee, Yan-Jiun and Yang, Yanyan and Lu, Tongxiang and Wheeler, Steven E. and Torres-Kolbus, Jessica and Deiters, Alexander and Liu, Wenshe R.}, year={2014}, month={Sep}, pages={1730–1738} }
 @article{govan_uprety_thomas_lusic_lively_deiters_2013, title={Cellular Delivery and Photochemical Activation of Antisense Agents through a Nucleobase Caging Strategy}, volume={8}, ISSN={["1554-8937"]}, DOI={10.1021/cb400293e}, abstractNote={Antisense oligonucleotides are powerful tools to regulate gene expression in cells and model organisms. However, a transfection or microinjection is typically needed for efficient delivery of the antisense agent. We report the conjugation of multiple HIV TAT peptides to a hairpin-protected antisense agent through a light-cleavable nucleobase caging group. This conjugation allows for the facile delivery of the antisense agent without a transfection reagent, and photochemical activation offers precise control over gene expression. The developed approach is highly modular, as demonstrated by the conjugation of folic acid to the caged antisense agent. This enabled targeted cell delivery through cell-surface folate receptors followed by photochemical triggering of antisense activity. Importantly, the presented strategy delivers native oligonucleotides after light-activation, devoid of any delivery functionalities or modifications that could otherwise impair their antisense activity.}, number={10}, journal={ACS CHEMICAL BIOLOGY}, author={Govan, Jeane M. and Uprety, Rajendra and Thomas, Meryl and Lusic, Hrvoje and Lively, Mark O. and Deiters, Alexander}, year={2013}, month={Oct}, pages={2272–2282} }
 @article{hemphill_deiters_2013, title={DNA Computation in Mammalian Cells: MicroRNA Logic Operations}, volume={135}, ISSN={["0002-7863"]}, DOI={10.1021/ja404350s}, abstractNote={DNA computation can utilize logic gates as modules to create molecular computers with biological inputs. Modular circuits that recognize nucleic acid inputs through strand hybridization activate computation cascades to produce controlled outputs. This allows for the construction of synthetic circuits that can be interfaced with cellular environments. We have engineered oligonucleotide AND gates to respond to specific microRNA (miRNA) inputs in live mammalian cells. Both single and dual-sensing miRNA-based computation devices were synthesized for the cell-specific identification of endogenous miR-21 and miR-122. A logic gate response was observed with miRNA expression regulators, exhibiting molecular recognition of miRNA profile changes. Nucleic acid logic gates that are functional in a cellular environment and recognize endogenous inputs significantly expand the potential of DNA computation to monitor, image, and respond to cell-specific markers.}, number={28}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Hemphill, James and Deiters, Alexander}, year={2013}, month={Jul}, pages={10512–10518} }
 @article{hemphill_chou_chin_deiters_2013, title={Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells}, volume={135}, DOI={10.1021/ja4051026}, abstractNote={Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference.}, number={36}, journal={Journal of the American Chemical Society}, author={Hemphill, J. and Chou, C. J. and Chin, J. W. and Deiters, A.}, year={2013}, pages={13433–13439} }
 @article{thomas_deiters_2013, title={MicroRNA miR-122 as a therapeutic target for oligonucleotides and small molecules}, volume={20}, DOI={10.2174/0929867311320290009}, abstractNote={The most abundant microRNA (miRNA) in the liver, miR-122, is regulated by specific, liver-enriched transcription factors and is responsible for proper proliferation and differentiation of hepatocytes and for the regulation of lipid and cholesterol metabolisms. miR-122 is also involved in several hepatic disorders, as downregulation of miR-122 is often associated with hepatocellular carcinoma (HCC) and miR-122 is a required component for the replication and proliferation of the hepatitis C virus (HCV). Various probes have been developed to promote a better understanding of the involvement of miR-122 in liver diseases, including modified antisense agents and small molecule inhibitors. These agents, capable of specifically modifying miR-122 activity, provide excellent tools to investigate the function and regulation of miR-122 and offer potential new lead compounds for drug discovery. Especially small molecule modifiers can display numerous advantages over nucleotide analogs, as discussed in this review.}, number={29}, journal={Current Medicinal Chemistry}, author={Thomas, M. and Deiters, A.}, year={2013}, pages={3629–3640} }
 @article{govan_young_lusic_liu_lively_deiters_2013, title={Optochemical control of RNA interference in mammalian cells}, volume={41}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkt806}, abstractNote={Short interfering RNAs (siRNAs) and microRNAs (miRNAs) have been widely used in mammalian tissue culture and model organisms to selectively silence genes of interest. One limitation of this technology is the lack of precise external control over the gene-silencing event. The use of photocleavable protecting groups installed on nucleobases is a promising strategy to circumvent this limitation, providing high spatial and temporal control over siRNA or miRNA activation. Here, we have designed, synthesized and site-specifically incorporated new photocaged guanosine and uridine RNA phosphoramidites into short RNA duplexes. We demonstrated the applicability of these photocaged siRNAs in the light-regulation of the expression of an exogenous green fluorescent protein reporter gene and an endogenous target gene, the mitosis motor protein, Eg5. Two different approaches were investigated with the caged RNA molecules: the light-regulation of catalytic RNA cleavage by RISC and the light-regulation of seed region recognition. The ability to regulate both functions with light enables the application of this optochemical methodology to a wide range of small regulatory RNA molecules.}, number={22}, journal={NUCLEIC ACIDS RESEARCH}, author={Govan, Jeane M. and Young, Douglas D. and Lusic, Hrvoje and Liu, Qingyang and Lively, Mark O. and Deiters, Alexander}, year={2013}, month={Dec}, pages={10518–10528} }
 @article{prokup_hemphill_deiters_2012, title={DNA Computation: A Photochemically Controlled AND Gate}, volume={134}, ISSN={["0002-7863"]}, DOI={10.1021/ja210050s}, abstractNote={DNA computation is an emerging field that enables the assembly of complex circuits based on defined DNA logic gates. DNA-based logic gates have previously been operated through purely chemical means, controlling logic operations through DNA strands or other biomolecules. Although gates can operate through this manner, it limits temporal and spatial control of DNA-based logic operations. A photochemically controlled AND gate was developed through the incorporation of caged thymidine nucleotides into a DNA-based logic gate. By using light as the logic inputs, both spatial control and temporal control were achieved. In addition, design rules for light-regulated DNA logic gates were derived. A step-response, which can be found in a controller, was demonstrated. Photochemical inputs close the gap between DNA computation and silicon-based electrical circuitry, since light waves can be directly converted into electrical output signals and vice versa. This connection is important for the further development of an interface between DNA logic gates and electronic devices, enabling the connection of biological systems with electrical circuits.}, number={8}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Prokup, Alex and Hemphill, James and Deiters, Alexander}, year={2012}, month={Feb}, pages={3810–3815} }
 @article{lang_davis_torres-kolbus_chou_deiters_chin_2012, title={Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction}, volume={4}, ISSN={["1755-4330"]}, DOI={10.1038/nchem.1250}, abstractNote={The site-specific incorporation of bioorthogonal groups via genetic code expansion provides a powerful general strategy for site-specifically labelling proteins with any probe. However, the slow reactivity of the bioorthogonal functional groups that can be encoded genetically limits the utility of this strategy. We demonstrate the genetic encoding of a norbornene amino acid using the pyrrolysyl tRNA synthetase/tRNA(CUA) pair in Escherichia coli and mammalian cells. We developed a series of tetrazine-based probes that exhibit 'turn-on' fluorescence on their rapid reaction with norbornenes. We demonstrate that the labelling of an encoded norbornene is specific with respect to the entire soluble E. coli proteome and thousands of times faster than established encodable bioorthogonal reactions. We show explicitly the advantages of this approach over state-of-the-art bioorthogonal reactions for protein labelling in vitro and on mammalian cells, and demonstrate the rapid bioorthogonal site-specific labelling of a protein on the mammalian cell surface.}, number={4}, journal={NATURE CHEMISTRY}, author={Lang, Kathrin and Davis, Lloyd and Torres-Kolbus, Jessica and Chou, Chungjung and Deiters, Alexander and Chin, Jason W.}, year={2012}, month={Apr}, pages={298–304} }
 @article{connelly_thomas_deiters_2012, title={High-Throughput Luciferase Reporter Assay for Small-Molecule Inhibitors of MicroRNA Function}, volume={17}, ISSN={["1087-0571"]}, DOI={10.1177/1087057112439606}, abstractNote={MicroRNAs (miRNAs) are endogenous, single-stranded, noncoding RNAs of 21 to 23 nucleotides that regulate gene expression, typically by binding the 3' untranslated regions of target messenger RNAs. It is estimated that miRNAs are involved in the regulation of 30% of all genes and almost every genetic pathway. Recently, the misregulation of miRNAs has been linked to various human diseases including cancer and viral infections, identifying miRNAs as potential targets for drug discovery. Thus, small-molecule modifiers of miRNAs could serve as lead structures for the development of new therapeutic agents and be useful tools in the elucidation of detailed mechanisms of miRNA function. As a result, we have developed a high-throughput screen for potential small-molecule regulators of the liver-specific microRNA miR-122, which is involved in hepatocellular carcinoma development and hepatitis C virus infection. Our small-molecule screen employs a Huh7 human hepatoma cell line stably transfected with a Renilla luciferase sensor for endogenous miR-122. The assay was optimized and validated using an miR-122 antisense agent and a previously identified small-molecule miR-122 inhibitor. The described reporter assay will enable the high-throughput screening of small-molecule miR-122 inhibitors and can be readily extended to other miRNAs.}, number={6}, journal={JOURNAL OF BIOMOLECULAR SCREENING}, author={Connelly, Colleen M. and Thomas, Meryl and Deiters, Alexander}, year={2012}, month={Jul}, pages={822–828} }
 @article{govan_mciver_riggsbee_deiters_2012, title={Hydrogen Peroxide Induced Activation of Gene Expression in Mammalian Cells using Boronate Estrone Derivatives}, volume={51}, ISSN={["1521-3773"]}, DOI={10.1002/anie.201203222}, abstractNote={Keeping the boron out of the ER: A genetic switch was engineered that activates gene expression in the presence of H2O2 (see scheme). The use of a boronate group on an estrone molecule allows for activation of gene expression through binding of the estrogen receptor only when the boron group is oxidized by H2O2. This sensor is highly sensitive and specific for H2O2. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.}, number={36}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Govan, Jeane M. and McIver, Andrew L. and Riggsbee, Chad and Deiters, Alexander}, year={2012}, pages={9066–9070} }
 @misc{gardner_deiters_2012, title={Light-controlled synthetic gene circuits}, volume={16}, ISSN={["1367-5931"]}, DOI={10.1016/j.cbpa.2012.04.010}, abstractNote={Highly complex synthetic gene circuits have been engineered in living organisms to develop systems with new biological properties. A precise trigger to activate or deactivate these complex systems is desired in order to tightly control different parts of a synthetic or natural network. Light represents an excellent tool to achieve this goal as it can be regulated in timing, location, intensity, and wavelength, which allows for precise spatiotemporal control over genetic circuits. Recently, light has been used as a trigger to control the biological function of small molecules, oligonucleotides, and proteins involved as parts in gene circuits. Light activation has enabled the construction of unique systems in living organisms such as band-pass filters and edge-detectors in bacterial cells. Additionally, light also allows for the regulation of intermediate steps of complex dynamic pathways in mammalian cells such as those involved in kinase networks. Herein we describe recent advancements in the area of light-controlled synthetic networks.}, number={3-4}, journal={CURRENT OPINION IN CHEMICAL BIOLOGY}, author={Gardner, Laura and Deiters, Alexander}, year={2012}, month={Aug}, pages={292–299} }
 @article{arbely_torres-kolbus_deiters_chin_2012, title={Photocontrol of Tyrosine Phosphorylation in Mammalian Cells via Genetic Encoding of Photocaged Tyrosine}, volume={134}, ISSN={["0002-7863"]}, DOI={10.1021/ja3046958}, abstractNote={We report the first site-specific genetic encoding of photocaged tyrosine into proteins in mammalian cells. By photocaging Tyr701 of STAT1 we demonstrate that it is possible to photocontrol tyrosine phosphorylation and signal transduction in mammalian cells.}, number={29}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Arbely, Eyal and Torres-Kolbus, Jessica and Deiters, Alexander and Chin, Jason W.}, year={2012}, month={Jul}, pages={11912–11915} }
 @article{govan_uprety_hemphill_lively_deiters_2012, title={Regulation of transcription through light-activation and light-deactivation of triplex-forming oligonucleotides in mammalian cells}, volume={7}, DOI={10.1021/cb300161r}, abstractNote={Triplex-forming oligonucleotides (TFOs) are efficient tools to regulate gene expression through the inhibition of transcription. Here, nucleobase-caging technology was applied to the temporal regulation of transcription through light-activated TFOs. Through site-specific incorporation of caged thymidine nucleotides, the TFO:DNA triplex formation is blocked, rendering the TFO inactive. However, after a brief UV irradiation, the caging groups are removed, activating the TFO and leading to the inhibition of transcription. Furthermore, the synthesis and site-specific incorporation of caged deoxycytidine nucleotides within TFO inhibitor sequences was developed, allowing for the light-deactivation of TFO function and thus photochemical activation of gene expression. After UV-induced removal of the caging groups, the TFO forms a DNA dumbbell structure, rendering it inactive, releasing it from the DNA, and activating transcription. These are the first examples of light-regulated TFOs and their application in the photochemical activation and deactivation of gene expression. In addition, hairpin loop structures were found to significantly increase the efficacy of phosphodiester DNA-based TFOs in tissue culture.}, number={7}, journal={ACS Chemical Biology}, author={Govan, J. M. and Uprety, R. and Hemphill, J. and Lively, M. O. and Deiters, A.}, year={2012}, pages={1247–1256} }
 @article{connelly_uprety_hemphill_deiters_2012, title={Spatiotemporal control of microRNA function using light-activated antagomirs}, volume={8}, ISSN={["1742-206X"]}, DOI={10.1039/c2mb25175b}, abstractNote={MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional gene regulators and have been shown to regulate many biological processes including embryonal development, cell differentiation, apoptosis, and proliferation. Variations in the expression of certain miRNAs have been linked to a wide range of human diseases - especially cancer - and the diversity of miRNA targets suggests that they are involved in various cellular networks. Several tools have been developed to control the function of individual miRNAs and have been applied to study their biogenesis, biological role, and therapeutic potential; however, common methods lack a precise level of control that allows for the study of miRNA function with high spatial and temporal resolution. Light-activated miRNA antagomirs for mature miR-122 and miR-21 were developed through the site-specific installation of caging groups on the bases of selected nucleotides. Installation of caged nucleotides led to complete inhibition of the antagomir-miRNA hybridization and thus inactivation of antagomir function. The miRNA-inhibitory activity of the caged antagomirs was fully restored upon decaging through a brief UV irradiation. The synthesized antagomirs were applied to the photochemical regulation of miRNA function in mammalian cells. Moreover, spatial control over antagomir activity was obtained in mammalian cells through localized UV exposure. The presented approach enables the precise regulation of miRNA function and miRNA networks with unprecedented spatial and temporal resolution using UV irradiation and can be extended to any miRNA of interest.}, number={11}, journal={MOLECULAR BIOSYSTEMS}, author={Connelly, Colleen M. and Uprety, Rajendra and Hemphill, James and Deiters, Alexander}, year={2012}, pages={2987–2993} }
 @article{morckel_lusic_farzana_yoder_deiters_nascone-yoder_2011, title={A photoactivatable small-molecule inhibitor for light-controlled spatiotemporal regulation of Rho kinase in live embryos}, volume={139}, ISSN={0950-1991 1477-9129}, url={http://dx.doi.org/10.1242/dev.072165}, DOI={10.1242/dev.072165}, abstractNote={To uncover the molecular mechanisms of embryonic development, the ideal loss-of-function strategy would be capable of targeting specific regions of the living embryo with both temporal and spatial precision. To this end, we have developed a novel pharmacological agent that can be light activated to achieve spatiotemporally limited inhibition of Rho kinase activity in vivo. A new photolabile caging group, 6-nitropiperonyloxymethyl (NPOM), was installed on a small-molecule inhibitor of Rho kinase, Rockout, to generate a ‘caged Rockout’ derivative. Complementary biochemical, cellular, molecular and morphogenetic assays in both mammalian cell culture and Xenopus laevis embryos validate that the inhibitory activity of the caged compound is dependent on exposure to light. Conveniently, this unique reagent retains many of the practical advantages of conventional small-molecule inhibitors, including delivery by simple diffusion in the growth medium and concentration-dependent tuneability, but can be locally activated by decaging with standard instrumentation. Application of this novel tool to the spatially heterogeneous problem of embryonic left-right asymmetry revealed a differential requirement for Rho signaling on the left and right sides of the primitive gut tube, yielding new insight into the molecular mechanisms that generate asymmetric organ morphology. As many aromatic/heterocyclic small-molecule inhibitors are amenable to installation of this caging group, our results indicate that photocaging pharmacological inhibitors might be a generalizable technique for engendering convenient loss-of-function reagents with great potential for wide application in developmental biology.}, number={2}, journal={Development}, publisher={The Company of Biologists}, author={Morckel, A. R. and Lusic, H. and Farzana, L. and Yoder, J. A. and Deiters, A. and Nascone-Yoder, N. M.}, year={2011}, month={Dec}, pages={437–442} }
 @article{zou_lin_maggard_deiters_2011, title={Efficacy of C-N Coupling Reactions with a New Multinuclear Copper Complex Catalyst and Its Dissociation into Mononuclear Species}, volume={2011}, ISSN={["1099-0690"]}, DOI={10.1002/ejoc.201100399}, abstractNote={A new tetranuclear copper(I)–pyridazine (pda)/rhenate hybrid has been synthesized under hydrothermal conditions and structurally characterized by X-ray crystallography. The activity of this catalyst, as well as its dissociation into mononuclear species, was investigated in homogeneous C–N arylation reactions. A variety of N-arylamides and -azoles were synthesized in good to excellent yields, revealing the effect of polynuclear versus mononuclear Cu complexation in this type of coupling reaction.}, number={22}, journal={EUROPEAN JOURNAL OF ORGANIC CHEMISTRY}, author={Zou, Yan and Lin, Haisheng and Maggard, Paul A. and Deiters, Alexander}, year={2011}, month={Aug}, pages={4154–4159} }
 @article{chou_uprety_davis_chin_deiters_2011, title={Genetically encoding an aliphatic diazirine for protein photocrosslinking}, volume={2}, ISSN={["2041-6539"]}, DOI={10.1039/c0sc00373e}, abstractNote={Photocrosslinking is an important approach that allows discovery and detailed investigation of protein–protein, protein–oligonucleotide, and protein–small molecule interactions with high temporal and spatial resolution. A major limitation to the universal application of this methodology is the site-specific introduction of efficient aliphatic photocrosslinking probes into proteins of interest. Here, we report a novel aliphatic diazirine amino acid and its genetically encoded, site-specific incorporation into proteins in bacterial and mammalian cells. Furthermore, we demonstrate efficient photocrosslinking of a test proteinin vitro and in vivo.}, number={3}, journal={CHEMICAL SCIENCE}, author={Chou, Chungjung and Uprety, Rajendra and Davis, Lloyd and Chin, Jason W. and Deiters, Alexander}, year={2011}, pages={480–483} }
 @article{dush_mciver_parr_young_fisher_newman_sannes_hauck_deiters_nascone-yoder_2011, title={Heterotaxin: A TGF-beta Signaling Inhibitor Identified in a Multi-Phenotype Profiling Screen in Xenopus Embryos}, volume={18}, ISSN={["1879-1301"]}, DOI={10.1016/j.chembiol.2010.12.008}, abstractNote={Disruptions of anatomical left-right asymmetry result in life-threatening heterotaxic birth defects in vital organs. We performed a small molecule screen for left-right asymmetry phenotypes in Xenopus embryos and discovered a pyridine analog, heterotaxin, which disrupts both cardiovascular and digestive organ laterality and inhibits TGF-β-dependent left-right asymmetric gene expression. Heterotaxin analogs also perturb vascular development, melanogenesis, cell migration, and adhesion, and indirectly inhibit the phosphorylation of an intracellular mediator of TGF-β signaling. This combined phenotypic profile identifies these compounds as a class of TGF-β signaling inhibitors. Notably, heterotaxin analogs also possess highly desirable antitumor properties, inhibiting epithelial-mesenchymal transition, angiogenesis, and tumor cell proliferation in mammalian systems. Our results suggest that assessing multiple organ, tissue, cellular, and molecular parameters in a whole organism context is a valuable strategy for identifying the mechanism of action of bioactive compounds.}, number={2}, journal={CHEMISTRY & BIOLOGY}, author={Dush, Michael K. and McIver, Andrew L. and Parr, Meredith A. and Young, Douglas D. and Fisher, Julie and Newman, Donna R. and Sannes, Philip L. and Hauck, Marlene L. and Deiters, Alexander and Nascone-Yoder, Nanette}, year={2011}, month={Feb}, pages={252–263} }
 @article{karginov_zou_shirvanyants_kota_dokholyan_young_hahn_deiters_2011, title={Light Regulation of Protein Dimerization and Kinase Activity in Living Cells Using Photocaged Rapamycin and Engineered FKBP}, volume={133}, ISSN={["0002-7863"]}, DOI={10.1021/ja109630v}, abstractNote={We developed a new system for light-induced protein dimerization in living cells using a photocaged analogue of rapamycin together with an engineered rapamycin binding domain. Using focal adhesion kinase as a target, we demonstrated successful light-mediated regulation of protein interaction and localization in living cells. Modification of this approach enabled light-triggered activation of a protein kinase and initiation of kinase-induced phenotypic changes in vivo.}, number={3}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Karginov, Andrei V. and Zou, Yan and Shirvanyants, David and Kota, Pradeep and Dokholyan, Nikolay V. and Young, Douglas D. and Hahn, Klaus M. and Deiters, Alexander}, year={2011}, month={Jan}, pages={420–423} }
 @article{chou_deiters_2011, title={Light-Activated Gene Editing with a Photocaged Zinc-Finger Nuclease}, volume={50}, ISSN={["1433-7851"]}, DOI={10.1002/anie.201101157}, abstractNote={A general approach for targeted gene modification with precise external control and high spatial and temporal resolution will greatly advance investigations in genetics, gene therapy, and developmental biology. However, traditional methods such as homologous recombination[1] and nonhomologous end joining[2] for the introduction and deletion of genomic DNA sequences usually display very low efficiency in vivo, thus limiting their applicability. Recently, the efficiency of these processes has been greatly improved by the ability to site-specifically introduce doublestrand breaks (DSBs) into genomic DNA.[3,4] A family of artificial restriction enzymes, namely zinc-finger nucleases (ZFN), has been developed to sequence-selectively achieve dsDNA scission. ZFNs have since emerged as important and widely recognized tools for the genetic modification of cells, model organisms, and possibly humans to investigate gene function and to treat genetic disorders.[5–9]}, number={30}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Chou, Chungjung and Deiters, Alexander}, year={2011}, pages={6839–6842} }
 @article{gautier_deiters_chin_2011, title={Light-Activated Kinases Enable Temporal Dissection of Signaling Networks in Living Cells}, volume={133}, ISSN={["1520-5126"]}, DOI={10.1021/ja1109979}, abstractNote={We report a general strategy for creating protein kinases in mammalian cells that are poised for very rapid activation by light. By photoactivating a caged version of MEK1, we demonstrate the specific, rapid, and receptor independent activation of an artificial subnetwork within the Raf/MEK/ERK pathway. Time-lapse microscopy allowed us to precisely characterize the kinetics of elementary steps in the signaling cascade and provided insight into adaptive feedback and rate-determining processes in the pathway.}, number={7}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Gautier, Arnaud and Deiters, Alexander and Chin, Jason W.}, year={2011}, month={Feb}, pages={2124–2127} }
 @article{govan_lively_deiters_2011, title={Photochemical Control of DNA Decoy Function Enables Precise Regulation of Nuclear Factor kappa B Activity}, volume={133}, ISSN={["0002-7863"]}, DOI={10.1021/ja204980v}, abstractNote={DNA decoys have been developed for the inhibition of transcriptional regulation of gene expression. However, the present methodology lacks the spatial and temporal control of gene expression that is commonly found in nature. Here, we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element. The NF-κB family of proteins is comprised of important eukaryotic transcription factors that regulate a wide range of cellular processes and are involved in immune response, development, cellular growth, and cell death. Several diseases, including cancer, arthritis, chronic inflammation, asthma, neurodegenerative diseases, and heart disease, have been linked to constitutively active NF-κB. Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide. Excellent light-switching behavior of transcriptional regulation was observed. This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells and represents an important addition to the toolbox of light-controlled gene regulatory agents.}, number={33}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Govan, Jeane M. and Lively, Mark O. and Deiters, Alexander}, year={2011}, month={Aug}, pages={13176–13182} }
 @article{gardner_zou_mara_cropp_deiters_2011, title={Photochemical control of bacterial signal processing using a light-activated erythromycin}, volume={7}, ISSN={["1742-206X"]}, DOI={10.1039/c1mb05166k}, abstractNote={Bacterial cells control resistance to the macrolide antibiotic erythromycin using the MphR(A) repressor protein. Erythromycin binds to MphR(A), causing release of the PmphR promoter, activating expression of the 2'-phosphotransferase Mph(A). We engineered the MphR(A)/promoter system to, in conjunction with a light-activatable derivative of erythromycin, enable photochemical activation of gene expression in E. coli. We applied this photochemical gene switch to the construction of a light-triggered logic gate, a light-controlled band-pass filter, as well as spatial and temporal control of gene expression.}, number={9}, journal={MOLECULAR BIOSYSTEMS}, author={Gardner, Laura and Zou, Yan and Mara, Alexandria and Cropp, T. Ashton and Deiters, Alexander}, year={2011}, pages={2554–2557} }
 @article{govan_mciver_deiters_2011, title={Stabilization and Photochemical Regulation of Antisense Agents through PEGylation}, volume={22}, ISSN={["1520-4812"]}, DOI={10.1021/bc200411n}, abstractNote={Oligonucleotides are effective tools for the regulation of gene expression in cell culture and model organisms, most importantly through antisense mechanisms. Due to the inherent instability of DNA antisense agents, various modifications have been introduced to increase the efficacy of oligonucleotides, including phosphorothioate DNA, locked nucleic acids, peptide nucleic acids, and others. Here, we present antisense agent stabilization through conjugation of a poly(ethylene glycol) (PEG) group to a DNA oligonucleotide. By employing a photocleavable linker between the PEG group and the antisense agent, we were able to achieve light-induced deactivation of antisense activity. The bioconjugated PEG group provides stability to the DNA antisense agent without affecting its native function of silencing gene expression via RNase H-catalyzed mRNA degradation. Once irradiated with UV light of 365 nm, the PEG group is cleaved from the antisense agent leaving the DNA unprotected and open for degradation by endogenous nucleases, thereby restoring gene expression. By using a photocleavable PEG group (PhotoPEG), antisense activity can be regulated with high spatial and temporal resolution, paving the way for precise regulation of gene expression in biological systems.}, number={10}, journal={BIOCONJUGATE CHEMISTRY}, author={Govan, Jeane M. and McIver, Andrew L. and Deiters, Alexander}, year={2011}, month={Oct}, pages={2136–2142} }
 @article{zou_liu_deiters_2011, title={Synthesis of the Pyridine Core of Cyclothiazomycin}, volume={13}, ISSN={["1523-7052"]}, DOI={10.1021/ol201682k}, abstractNote={A highly convergent synthesis of the pyridine core of the thiopeptide antibiotic cyclothiazomycin has been developed based on a [2+2+2] cyclotrimerization key step. The regioselective assembly of the heterocyclic center of this important class of antibiotics takes advantage of a temporary silicon tether and the ruthenium-catalyzed cyclotrimerization reaction of a diyne and an electron-poor thiazole nitrile.}, number={16}, journal={ORGANIC LETTERS}, author={Zou, Yan and Liu, Qingyang and Deiters, Alexander}, year={2011}, month={Aug}, pages={4352–4355} }
 @article{bilbille_gustilo_harris_jones_lusic_kaiser_delano_spremulli_deiters_agris_2011, title={The Human Mitochondrial tRNA(Met): Structure/Function Relationship of a Unique Modification in the Decoding of Unconventional Codons}, volume={406}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2010.11.042}, abstractNote={Human mitochondrial mRNAs utilize the universal AUG and the unconventional isoleucine AUA codons for methionine. In contrast to translation in the cytoplasm, human mitochondria use one tRNA, hmtRNAMetCAU, to read AUG and AUA codons at both the peptidyl- (P-), and aminoacyl- (A-) sites of the ribosome. The hmtRNAMetCAU has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position 34 (f5C34), and a cytidine substituting for the invariant uridine at position 33 of the canonical U-turn in tRNAs. The structure of the tRNA anticodon stem and loop domain (hmtASLMetCAU), determined by NMR restrained molecular modeling, revealed how the f5C34 modification facilitates the decoding of AUA at the P- and the A-sites. The f5C34 defined a reduced conformational space for the nucleoside, in what appears to have restricted the conformational dynamics of the anticodon bases of the modified hmtASLMetCAU. The hmtASLMetCAU exhibited a C-turn conformation that has some characteristics of the U-turn motif. Codon binding studies with both Escherichia coli and bovine mitochondrial ribosomes revealed that the f5C34 facilitates AUA binding in the A-site and suggested that the modification favorably alters the ASL binding kinetics. Mitochondrial translation by many organisms, including humans, sometimes initiates with the universal isoleucine codons AUU and AUC. The f5C34 enabled P-site codon binding to these normally isoleucine codons. Thus, the physicochemical properties of this one modification, f5C34, expand codon recognition from the traditional AUG to the non-traditional, synonymous codons AUU and AUC as well as AUA, in the reassignment of universal codons in the mitochondria.}, number={2}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Bilbille, Yann and Gustilo, Estella M. and Harris, Kimberly A. and Jones, Christie N. and Lusic, Hrvoje and Kaiser, Robert J. and Delano, Michael O. and Spremulli, Linda L. and Deiters, Alexander and Agris, Paul F.}, year={2011}, month={Feb}, pages={257–274} }
 @article{young_lively_deiters_2010, title={Activation and Deactivation of DNAzyme and Antisense Function with Light for the Photochemical Regulation of Gene Expression in Mammalian Cells}, volume={132}, ISSN={["1520-5126"]}, DOI={10.1021/ja100710j}, abstractNote={The photochemical regulation of biological systems represents a very precise means of achieving high-resolution control over gene expression in both a spatial and a temporal fashion. DNAzymes are enzymatically active deoxyoligonucleotides that enable the site-specific cleavage of RNA and have been used in a variety of in vitro applications. We have previously reported the photochemical activation of DNAzymes and antisense agents through the preparation of a caged DNA phosphoramidite and its site-specific incorporation into oligonucleotides. The presence of the caging group disrupts either DNA:RNA hybridization or catalytic activity until removed via a brief irradiation with UV light. Here, we are expanding this concept by investigating the photochemical deactivation of DNAzymes and antisense agents. Moreover, we report the application of light-activated and light-deactivated antisense agents to the regulation of gene function in mammalian cells. This represents the first example of gene silencing antisense agents that can be turned on and turned off in mammalian tissue culture.}, number={17}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Young, Douglas D. and Lively, Mark O. and Deiters, Alexander}, year={2010}, month={May}, pages={6183–6193} }
 @article{hancock_uprety_deiters_chin_2010, title={Expanding the Genetic Code of Yeast for Incorporation of Diverse Unnatural Amino Acids via a Pyrrolysyl-tRNA Synthetase/tRNA Pair}, volume={132}, ISSN={["0002-7863"]}, DOI={10.1021/ja104609m}, abstractNote={We report the discovery of a simple system through which variant pyrrolysyl-tRNA synthetase/tRNACUAPyl pairs created in Escherichia coli can be used to expand the genetic code of Saccharomyces cerevisiae. In the process we have solved the key challenges of producing a functional tRNACUAPyl in yeast and discovered a pyrrolysyl-tRNA synthetase/tRNACUAPyl pair that is orthogonal in yeast. Using our approach we have incorporated an alkyne-containing amino acid for click chemistry, an important post-translationally modified amino acid and one of its analogs, a photocaged amino acid and a photo-cross-linking amino acid into proteins in yeast. Extensions of our approach will allow the growing list of useful amino acids that have been incorporated in E. coli with variant pyrrolysyl-tRNA synthetase/tRNACUAPyl pairs to be site-specifically incorporated into proteins in yeast.}, number={42}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Hancock, Susan M. and Uprety, Rajendra and Deiters, Alexander and Chin, Jason W.}, year={2010}, month={Oct}, pages={14819–14824} }
 @article{miyake-stoner_refakis_hammill_lusic_hazen_deiters_mehl_2010, title={Generating Permissive Site-Specific Unnatural Aminoacyl-tRNA Synthetases}, volume={49}, ISSN={["0006-2960"]}, DOI={10.1021/bi901947r}, abstractNote={Genetically incorporated unnatural amino acid (UAA) technologies are powerful tools that are greatly enhancing our ability to study and engineer biological systems. Using these techniques, researchers can precisely control the position and number of novel chemical moieties in a protein, via introducing the novel R group of UAAs, that are genetically encoded in the protein’s primary structure. The substrate recognition properties of a natural aminoacyl-tRNA synthetase (aaRS) must be modified in order to incorporate UAAs into proteins. Protocols to do so are technically simple but require time and optimization, which has significantly limited the accessibility of this important technology. At present, engineered unnatural aminoacyl-tRNA synthetases (UaaRS) are evaluated on their translational efficiency (the extent to which they allow for incorporation of UAAs into protein) and fidelity (the extent to which they prevent incorporation of natural amino acids). We propose that a third parameter of substrate recognition, permissivity, is equally important. Permissive UaaRSs, whose relaxed substrate recognition properties allow them to incorporate multiple unnatural amino acids (but not natural amino acids), would eliminate the need to generate new UaaRSs for many new UAAs. Here, we outline methods for quickly and easily assessing the permissivity of existing UaaRSs and for generating permissive UaaRSs. In proof of principle experiments, we determined the degree of permissivity of two UaaRSs for a family of structurally related fluorinated UAAs (19F-UAAs). We then increased the permissivity of the initial UaaRSs to allow for incorporation of the family of 19F-UAAs. Finally, we validated the utility of these new 19F-UAAs as probes for fluorine NMR studies of protein structure and dynamics. We expect that results of this work will increase the accessibility of UAA technology and the use of new UAAs in proteins.}, number={8}, journal={BIOCHEMISTRY}, author={Miyake-Stoner, Shigeki J. and Refakis, Christian A. and Hammill, Jared T. and Lusic, Hrvoje and Hazen, Jennifer L. and Deiters, Alexander and Mehl, Ryan A.}, year={2010}, month={Mar}, pages={1667–1677} }
 @article{gautier_nguyen_lusic_an_deiters_chin_2010, title={Genetically encoded photocontrol of protein localization in mammalian cells}, volume={132}, number={12}, journal={Journal of the American Chemical Society}, author={Gautier, A. and Nguyen, D. P. and Lusic, H. and An, W. A. and Deiters, A. and Chin, J. W.}, year={2010}, pages={4086-} }
 @article{lusic_uprety_deiters_2010, title={Improved Synthesis of the Two-Photon Caging Group 3-Nitro-2-Ethyldibenzofuran and Its Application to a Caged Thymidine Phosphoramidite}, volume={12}, ISSN={["1523-7060"]}, DOI={10.1021/ol902807q}, abstractNote={A new and efficient route to the recently reported 3-nitro-2-ethyldibenzofuran caging group was developed. Furthermore, its installation on a thymidine phosphoramidite is described. This caging group is efficiently removed through light-irradiation at 365 nm.}, number={5}, journal={ORGANIC LETTERS}, author={Lusic, Hrvoje and Uprety, Rajendra and Deiters, Alexander}, year={2010}, month={Mar}, pages={916–919} }
 @article{deiters_garner_lusic_govan_dush_nascone-yoder_yoder_2010, title={Photocaged Morpholino Oligomers for the Light-Regulation of Gene Function in Zebrafish and Xenopus Embryos}, volume={132}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja1053863}, DOI={10.1021/ja1053863}, abstractNote={Morpholino oligonucleotides, or morpholinos, have emerged as powerful antisense reagents for evaluating gene function in both in vitro and in vivo contexts. However, the constitutive activity of these reagents limits their utility for applications that require spatiotemporal control, such as tissue-specific gene disruptions in embryos. Here we report a novel and efficient synthetic route for incorporating photocaged monomeric building blocks directly into morpholino oligomers and demonstrate the utility of these caged morpholinos in the light-activated control of gene function in both cell culture and living embryos. We demonstrate that a caged morpholino that targets enhanced green fluorescent protein (EGFP) disrupts EGFP production only after exposure to UV light in both transfected cells and living zebrafish (Danio rerio) and Xenopus frog embryos. Finally, we show that a caged morpholino targeting chordin, a zebrafish gene that yields a distinct phenotype when functionally disrupted by conventional morpholinos, elicits a chordin phenotype in a UV-dependent manner. Our results suggest that photocaged morpholinos are readily synthesized and highly efficacious tools for light-activated spatiotemporal control of gene expression in multiple contexts.}, number={44}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Deiters, Alexander and Garner, R. Aaron and Lusic, Hrvoje and Govan, Jeane M. and Dush, Mike and Nascone-Yoder, Nanette M. and Yoder, Jeffrey A.}, year={2010}, month={Nov}, pages={15644–15650} }
 @article{chou_young_deiters_2010, title={Photocaged T7 RNA Polymerase for the Light Activation of Transcription and Gene Function in Pro- and Eukaryotic Cells}, volume={11}, ISSN={["1439-7633"]}, DOI={10.1002/cbic.201000041}, abstractNote={A light-activatable bacteriophage T7 RNA polymerase (T7RNAP) has been generated through the site-specific introduction of a photocaged tyrosine residue at the crucial position Tyr639 within the active site of the enzyme. The photocaged tyrosine disrupts polymerase activity by blocking the incoming nucleotide from reaching the active site of the enzyme. However, a brief irradiation with nonphototoxic UV light of 365 nm removes the ortho-nitrobenzyl caging group from Tyr639 and restores the RNA polymerase activity of T7RNAP. The complete orthogonality of T7RNAP to all endogenous RNA polymerases in pro- and eukaryotic systems allowed for the photochemical activation of gene expression in bacterial and mammalian cells. Specifically, E. coli cells were engineered to produce photocaged T7RNAP in the presence of a GFP reporter gene under the control of a T7 promoter. UV irradiation of these cells led to the spatiotemporal activation of GFP expression. In an analogous fashion, caged T7RNAP was transfected into human embryonic kidney (HEK293T) cells. Irradiation with UV light led to the activation of T7RNAP, thereby inducing RNA polymerization and expression of a luciferase reporter gene in tissue culture. The ability to achieve spatiotemporal regulation of orthogonal RNA synthesis enables the precise dissection and manipulation of a wide range of cellular events, including gene function.}, number={7}, journal={CHEMBIOCHEM}, author={Chou, Chungjung and Young, Douglas D. and Deiters, Alexander}, year={2010}, month={May}, pages={972–977} }
 @article{georgianna_lusic_mclver_deiters_2010, title={Photocleavable Polyethylene Glycol for the Light-Regulation of Protein Function}, volume={21}, ISSN={["1043-1802"]}, DOI={10.1021/bc100084n}, abstractNote={PEGylation is commonly employed to enhance the pharmacokinetic properties of proteins, but it can interfere with natural protein function. Protein activity can thus be abrogated through PEGylation, and a controllable means to remove the polyethylene glycol (PEG) group from the protein is desirable. As such, light affords a unique control over biomolecules through the application of photosensitive groups. Herein, we report the synthesis of a photocleavable PEG reagent (PhotoPEG) and its application to the light-regulation of enzyme activity.}, number={8}, journal={BIOCONJUGATE CHEMISTRY}, author={Georgianna, Wesleigh E. and Lusic, Hrvoje and Mclver, Andrew L. and Deiters, Alexander}, year={2010}, month={Aug}, pages={1404–1407} }
 @article{deiters_2010, title={Principles and Applications of the Photochemical Control of Cellular Processes}, volume={11}, ISSN={["1439-4227"]}, DOI={10.1002/cbic.200900529}, abstractNote={In the cage: Photochemical control over biological processes is commonly achieved with caged molecules. While the first reported examples of caged compounds were small molecules, recent advances in caging technologies have enabled the photochemical regulation of oligonucleotide and protein function. This article discusses different approaches to the caging of small molecules, DNA, and proteins, and the requirements for efficient light regulation of cellular processes by using caged molecules.}, number={1}, journal={CHEMBIOCHEM}, author={Deiters, Alexander}, year={2010}, month={Jan}, pages={47–53} }
 @misc{riggsbee_deiters_2010, title={Recent advances in the photochemical control of protein function}, volume={28}, ISSN={["1879-3096"]}, DOI={10.1016/j.tibtech.2010.06.001}, abstractNote={Biological processes are regulated with a high level of spatial and temporal resolution. To understand and manipulate these processes, scientists need to be able to regulate them with Nature's level of precision. In this context, light is a unique regulatory element because it can be precisely controlled in terms of location, timing and amplitude. Moreover, most biological laboratories have a wide range of light sources as standard equipment. This review article summarizes the most recent advances in light-mediated regulation of protein function and its application in a cellular context. Specifically, the photocaging of small-molecule modulators of protein function and of specific amino acid residues in proteins is discussed. In addition, examples of the photochemical control of protein function through the application of genetically engineered natural-light receptors are presented. Biological processes are regulated with a high level of spatial and temporal resolution. To understand and manipulate these processes, scientists need to be able to regulate them with Nature's level of precision. In this context, light is a unique regulatory element because it can be precisely controlled in terms of location, timing and amplitude. Moreover, most biological laboratories have a wide range of light sources as standard equipment. This review article summarizes the most recent advances in light-mediated regulation of protein function and its application in a cellular context. Specifically, the photocaging of small-molecule modulators of protein function and of specific amino acid residues in proteins is discussed. In addition, examples of the photochemical control of protein function through the application of genetically engineered natural-light receptors are presented.}, number={9}, journal={TRENDS IN BIOTECHNOLOGY}, author={Riggsbee, Chad W. and Deiters, Alexander}, year={2010}, month={Sep}, pages={468–475} }
 @article{georgianna_deiters_2010, title={Reversible light switching of cell signalling by genetically encoded protein dimerization}, volume={11}, DOI={10.1002/cbic.200900754}, abstractNote={Let there be light! Light control provides precise spatial and temporal regulation of cellular events. A genetically encoded system based on the photoswitchable Arabidopsis thaliana PhyB–PIF interaction has been applied to the reversible photocontrol of protein translocation and cellular morphology in mammalian cells.}, number={3}, journal={Chembiochem}, author={Georgianna, W. E. and Deiters, A.}, year={2010}, pages={301–303} }
 @article{wilkins_marionni_young_liu_wang_di salvo_deiters_cropp_2010, title={Site-Specific Incorporation of Fluorotyrosines into Proteins in Escherichia coli by Photochemical Disguise}, volume={49}, ISSN={["0006-2960"]}, DOI={10.1021/bi100013s}, abstractNote={Fluorinated analogues of tyrosine can be used to manipulate the electronic environments of protein active sites. The ability to selectively mutate tyrosine residues to fluorotyrosines is limited, however, and can currently only be achieved through the total synthesis of proteins. As a general solution to this problem, we genetically encoded the unnatural amino acids o-nitrobenzyl-2-fluorotyrosine, -3-fluorotyrosine, and -2,6-difluorotyrosine in Escherichia coli. These amino acids are disguised from recognition by the endogenous protein biosynthetic machinery, effectively preventing global incorporation of fluorotyrosine into proteins.}, number={8}, journal={BIOCHEMISTRY}, author={Wilkins, Bryan J. and Marionni, Samuel and Young, Douglas D. and Liu, Jia and Wang, Yan and Di Salvo, Martino L. and Deiters, Alexander and Cropp, T. Ashton}, year={2010}, month={Mar}, pages={1557–1559} }
 @article{young_connelly_grohmann_deiters_2010, title={Small Molecule Modifiers of MicroRNA miR-122 Function for the Treatment of Hepatitis C Virus Infection and Hepatocellular Carcinoma}, volume={132}, ISSN={["1520-5126"]}, DOI={10.1021/ja910275u}, abstractNote={MicroRNAs are a recently discovered new class of important endogenous regulators of gene function. Aberrant regulation of microRNAs has been linked to various human diseases, most importantly cancer. Small molecule intervention of microRNA misregulation has the potential to provide new therapeutic approaches to such diseases. Here, we report the first small molecule inhibitors and activators of the liver-specific microRNA miR-122. This microRNA is the most abundant microRNA in the liver and is involved in hepatocellular carcinoma development and hepatitis C virus (HCV) infection. Our small molecule inhibitors reduce viral replication in liver cells and represent a new approach to the treatment of HCV infections. Moreover, small molecule activation of miR-122 in liver cancer cells selectively induced apoptosis through caspase activation, thus having implications in cancer chemotherapy. In addition to providing a new approach for the development of therapeutics, small molecule modifiers of miR-122 function are unique tools for exploring miR-122 biogenesis.}, number={23}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Young, Douglas D. and Connelly, Colleen M. and Grohmann, Christoph and Deiters, Alexander}, year={2010}, month={Jun}, pages={7976–7981} }
 @misc{deiters_2010, title={Small Molecule Modifiers of the microRNA and RNA Interference Pathway}, volume={12}, ISSN={["1550-7416"]}, DOI={10.1208/s12248-009-9159-3}, abstractNote={Recently, the RNA interference (RNAi) pathway has become the target of small molecule inhibitors and activators. RNAi has been well established as a research tool in the sequence-specific silencing of genes in eukaryotic cells and organisms by using exogenous, small, double-stranded RNA molecules of approximately 20 nucleotides. Moreover, a recently discovered post-transcriptional gene regulatory mechanism employs microRNAs (miRNAs), a class of endogenously expressed small RNA molecules, which are processed via the RNAi pathway. The chemical modulation of RNAi has important therapeutic relevance, because a wide range of miRNAs has been linked to a variety of human diseases, especially cancer. Thus, the activation of tumor-suppressive miRNAs and the inhibition of oncogenic miRNAs by small molecules have the potential to provide a fundamentally new approach for the development of cancer therapeutics.}, number={1}, journal={AAPS JOURNAL}, author={Deiters, Alexander}, year={2010}, month={Mar}, pages={51–60} }
 @article{zou_deiters_2010, title={Total Synthesis of Cryptoacetalide}, volume={75}, ISSN={["1520-6904"]}, DOI={10.1021/jo100867v}, abstractNote={We are reporting the first total synthesis of the tetracyclic terpene natural product cryptoacetalide. Key steps of the synthesis are a microwave-mediated [2+2+2] cyclo-trimerization reaction to construct the central benzene ring, and a light-mediated radical cyclization to assemble the spiro-ketal moiety.}, number={15}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Zou, Yan and Deiters, Alexander}, year={2010}, month={Aug}, pages={5355–5358} }
 @article{mciver_deiters_2010, title={Tricyclic Alkaloid Core Structures Assembled by a Cyclotrimerization-Coupled Intramolecular Nucleophilic Substitution Reaction}, volume={12}, ISSN={["1523-7052"]}, DOI={10.1021/ol100177u}, abstractNote={A facile approach to tricyclic alkaloid core structures was developed by sequencing a pyridine-forming [2 + 2 + 2] cyclotrimerization reaction with an intramolecular nucleophilic substitution. This methodology enabled the facile assembly of the spiroindolinone framework of citrinadins A and B, and cyclopiamine B.}, number={6}, journal={ORGANIC LETTERS}, author={McIver, Andrew L. and Deiters, Alexander}, year={2010}, month={Mar}, pages={1288–1291} }
 @article{chou_young_deiters_2009, title={A Light-Activated DNA Polymerase}, volume={48}, ISSN={["1521-3773"]}, DOI={10.1002/anie.200901115}, abstractNote={When the time is right: The widely applied Thermus aquaticus DNA polymerase was rendered light-activatable by incorporation of the photocaged amino acid ortho-nitrobenzyl tyrosine in place of a key tyrosine residue in the active site (see picture). As the modified enzyme was completely inactive until irradiated with UV light, temporal regulation of polymerase activity was possible.}, number={32}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Chou, Chungjung and Young, Douglas D. and Deiters, Alexander}, year={2009}, pages={5950–5953} }
 @article{bereman_young_deiters_muddiman_2009, title={Development of a Robust and High Throughput Method for Profiling N-Linked Glycans Derived from Plasma Glycoproteins by NanoLC-FTICR Mass Spectrometry}, volume={8}, ISSN={["1535-3907"]}, DOI={10.1021/pr9002323}, abstractNote={Recent investigations continue to emphasize the importance of glycosylation in various diseases including cancer. In this work, we present a step-by-step protocol describing a method for N-linked glycan profiling of plasma glycoproteins by nanoflow liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). A large experimental space was initially explored and is described herein. Three internal standards were spiked into the sample and provided normalization of plasma glycan abundance across different experimental conditions. Incubation methods and times and the effect of NP40 detergent on glycan abundance were explored. It was found that an 18-h incubation with no detergent led to the greatest ion abundance; however, data could be obtained in less than one day from raw plasma samples utilizing microwave irradiation or shorter incubation periods. The intersample precision of three different glycans was less than 5.5% (RSD) when the internal standards were added prior to the initial processing step. The high mass measurement accuracy (<3 ppm) afforded by the FTICR mass spectrometer provided confident identifications of several glycan species.}, number={7}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Bereman, Michael S. and Young, Douglas D. and Deiters, Alexander and Muddiman, David C.}, year={2009}, month={Jul}, pages={3764–3770} }
 @article{nguyen_lusic_neumann_kapadnis_deiters_chin_2009, title={Genetic Encoding and Labeling of Aliphatic Azides and Alkynes in Recombinant Proteins via a Pyrrolysyl-tRNA Synthetase/tRNA(CUA) Pair and Click Chemistry}, volume={131}, ISSN={["0002-7863"]}, DOI={10.1021/ja900553w}, abstractNote={We demonstrate that an orthogonal Methanosarcina barkeri MS pyrrolysyl-tRNA synthetase/tRNA(CUA) pair directs the efficient, site-specific incorporation of N6-[(2-propynyloxy)carbonyl]-L-lysine, containing a carbon-carbon triple bond, and N6-[(2-azidoethoxy)carbonyl]-L-lysine, containing an azido group, into recombinant proteins in Escherichia coli. Proteins containing the alkyne functional group are labeled with an azido biotin and an azido fluorophore, via copper catalyzed [3+2] cycloaddition reactions, to produce the corresponding triazoles in good yield. The methods reported are useful for the site-specific labeling of recombinant proteins and may be combined with mutually orthogonal methods of introducing unnatural amino acids into proteins as well as with chemically orthogonal methods of protein labeling. This should allow the site specific incorporation of multiple distinct probes into proteins and the control of protein topology and structure by intramolecular orthogonal conjugation reactions.}, number={25}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Nguyen, Duy P. and Lusic, Hrvoje and Neumann, Heinz and Kapadnis, Prashant B. and Deiters, Alexander and Chin, Jason W.}, year={2009}, month={Jul}, pages={8720-+} }
 @misc{deiters_2009, title={Light activation as a method of regulating and studying gene expression}, volume={13}, ISSN={["1879-0402"]}, DOI={10.1016/j.cbpa.2009.09.026}, abstractNote={Recently, several advances have been made in the activation and deactivation of gene expression using light. These developments are based on the application of small molecule inducers of gene expression, antisense- or RNA interference-mediated gene silencing, and the photochemical control of proteins regulating gene function. The majority of the examples employ a classical 'caging technology', through the chemical installation of a light-removable protecting group on the biological molecule (small molecule, oligonucleotide, or protein) of interest and rendering it inactive. UV light irradiation then removes the caging group and activates the molecule, enabling control over gene activity with high spatial and temporal resolution.}, number={5-6}, journal={CURRENT OPINION IN CHEMICAL BIOLOGY}, author={Deiters, Alexander}, year={2009}, month={Dec}, pages={678–686} }
 @article{edwards_young_deiters_2009, title={Light-Activated Cre Recombinase as a Tool for the Spatial and Temporal Control of Gene Function in Mammalian Cells}, volume={4}, ISSN={["1554-8937"]}, DOI={10.1021/cb900041s}, abstractNote={Cre recombinase catalyzes DNA exchange between two conserved lox recognition sites. The enzyme has extensive biological application, from basic cloning to engineering knock-out and knock-in organisms. Widespread use of Cre is due to its simplicity and effectiveness, but the enzyme and the recombination event remain difficult to control with high precision. To obtain such control we report the installation of a light-responsive o-nitrobenzyl caging group directly in the catalytic site of Cre, inhibiting its activity. Prior to irradiation, caged Cre is completely inactive, as demonstrated both in vitro and in mammalian cell culture. Exposure to non-damaging UVA light removes the caging group and restores recombinase activity. Tight spatio-temporal control over DNA recombination is thereby achieved.}, number={6}, journal={ACS CHEMICAL BIOLOGY}, author={Edwards, Wesleigh F. and Young, Douglas D. and Deiters, Alexander}, year={2009}, month={Jun}, pages={441–445} }
 @article{young_garner_yoder_deiters_2009, title={Light-activation of gene function in mammalian cells via ribozymes}, ISSN={1359-7345 1364-548X}, url={http://dx.doi.org/10.1039/b819375d}, DOI={10.1039/b819375d}, abstractNote={A ribozyme based gene control element enabled the spatio-temporal regulation of gene function in mammalian cell culture with light.}, number={5}, journal={Chem. Commun.}, publisher={Royal Society of Chemistry (RSC)}, author={Young, Douglas D. and Garner, R. Aaron and Yoder, Jeffrey A. and Deiters, Alexander}, year={2009}, pages={568–570} }
 @article{young_teske_deiters_2009, title={Open-Vessel Microwave-Mediated [2+2+2]-Cyclotrimerization Reactions}, ISSN={["1437-210X"]}, DOI={10.1055/s-0029-1218149}, abstractNote={[2+2+2]-Cyclotrimerization reactions often suffer from low reaction rates and low chemoselectivity. We are reporting a solution to both problems through the use of open-vessel conditions for microwave-mediated cyclotrimerization reactions.}, number={22}, journal={SYNTHESIS-STUTTGART}, author={Young, Douglas D. and Teske, Jesse A. and Deiters, Alexander}, year={2009}, month={Nov}, pages={3785–3790} }
 @article{young_govan_lively_deiters_2009, title={Photochemical Regulation of Restriction Endonuclease Activity}, volume={10}, ISSN={["1439-7633"]}, DOI={10.1002/cbic.200900090}, abstractNote={Removal by the light: The photochemical regulation of restriction endonucleases, which are important enzymes in molecular biology, has been investigated. Photolabile protecting groups have been installed on DNA substrates and have been demonstrated to inhibit restriction endonuclease activity until removed by UV light irradiation. Interestingly, these groups do not appear to dramatically affect initial binding of the enzyme to the DNA substrate, but rather prevent recognition of the specific cleavage site.}, number={10}, journal={CHEMBIOCHEM}, author={Young, Douglas D. and Govan, Jeane M. and Lively, Mark O. and Deiters, Alexander}, year={2009}, month={Jul}, pages={1612–1616} }
 @article{young_lusic_lively_deiters_2009, title={Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization}, volume={37}, number={8}, journal={Nucleic Acids Research}, author={Young, D. D. and Lusic, H. and Lively, M. O. and Deiters, A.}, year={2009} }
 @article{edwards_young_deiters_2009, title={The effect of microwave irradiation on DNA hybridization}, volume={7}, ISSN={["1477-0539"]}, DOI={10.1039/b903609a}, abstractNote={The effect of microwave irradiation on DNA/DNA hybridization has been studied under controlled power and temperature conditions. It was discovered that microwave irradiation led to the melting of double-stranded deoxyoligonucleotides well below their thermal melting temperature and independent of the length of the deoxyoligonucleotides. These observations indicate a specific interaction of microwaves with DNA, and have important implications in the chemical or enzymatic processing of DNA under microwave heating.}, number={12}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Edwards, Wesleigh F. and Young, Douglas D. and Deiters, Alexander}, year={2009}, pages={2506–2508} }
 @article{teske_deiters_2008, title={A cyclotrimerization route to cannabinoids}, volume={10}, ISSN={["1523-7052"]}, DOI={10.1021/ol800589e}, abstractNote={Three members of the cannabinoid class, cannabinol, cannabinol methyl ether, and cannabinodiol, were synthesized using a microwave-mediated [2 + 2 + 2] cyclotrimerization reaction as the key step. This approach provides a high level of synthetic flexibility allowing for the facile synthesis of cannabinoid analogues.}, number={11}, journal={ORGANIC LETTERS}, author={Teske, Jesse A. and Deiters, Alexander}, year={2008}, month={Jun}, pages={2195–2198} }
 @article{mciver_young_deiters_2008, title={A general approach to triphenylenes and azatriphenylenes: total synthesis of dehydrotylophorine and tylophorine}, ISSN={["1359-7345"]}, DOI={10.1039/b811068a}, abstractNote={A convergent and flexible synthesis of substituted triphenylenes, azatriphenylenes, and the cytotoxic alkaloids dehydrotylophorine and tylophorine has been developed.}, number={39}, journal={CHEMICAL COMMUNICATIONS}, author={McIver, Andrew and Young, Douglas D. and Deiters, Alexander}, year={2008}, pages={4750–4752} }
 @article{young_lusic_lively_yoder_deiters_2008, title={Gene Silencing in Mammalian Cells with Light-Activated Antisense Agents}, volume={9}, ISSN={1439-4227 1439-7633}, url={http://dx.doi.org/10.1002/cbic.200800627}, DOI={10.1002/cbic.200800627}, abstractNote={On and off the spot: The spatio-temporal light-activation of gene silencing was achieved through the complete inactivation of phosphorothioate antisense agents by installing light-removable (caged) groups at specific sites, as illustrated here. Full antisense activity was restored through a brief irradiation with UV light at 365 nm.}, number={18}, journal={ChemBioChem}, publisher={Wiley}, author={Young, Douglas D. and Lusic, Hrvoje and Lively, Mark O. and Yoder, Jeffrey A. and Deiters, Alexander}, year={2008}, month={Dec}, pages={2937–2940} }
 @article{lusic_lively_deiters_2008, title={Light-activated deoxyguanosine: photochemical regulation of peroxidase activity}, volume={4}, ISSN={["1742-206X"]}, DOI={10.1039/b800166a}, abstractNote={Photochemical activation of a deoxyribozyme with peroxidase activity was achieved by the synthesis and incorporation of a caged deoxyguanosine.}, number={6}, journal={MOLECULAR BIOSYSTEMS}, author={Lusic, Hrvoje and Lively, Mark O. and Deiters, Alexander}, year={2008}, pages={508–511} }
 @article{young_deiters_2008, title={Light-regulated RNA-small molecule interactions}, volume={9}, ISSN={["1439-4227"]}, DOI={10.1002/cbic.200800051}, abstractNote={Regulating RNA with light. An RNA aptamer capable of specifically binding one isomer of a photoisomerizable spiropyran small molecule was engineered. The reversibility of the light-switchable aptamer recognition was then characterized by SPR imaging. This RNA–small molecule pair has significant implications in the light-regulation of biological functions and the reversible control of gene expression. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2008/z800051_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.}, number={8}, journal={CHEMBIOCHEM}, author={Young, Douglas D. and Deiters, Alexander}, year={2008}, month={May}, pages={1225–1228} }
 @article{young_edwards_lusic_lively_deiters_2008, title={Light-triggered polymerase chain reaction}, ISSN={["1364-548X"]}, DOI={10.1039/b715152g}, abstractNote={Photochemical control of the polymerase chain reaction has been achieved through the incorporation of light-triggered nucleotides into DNA.}, number={4}, journal={CHEMICAL COMMUNICATIONS}, author={Young, Douglas D. and Edwards, Wesleigh F. and Lusic, Hrvoje and Lively, Mark O. and Deiters, Alexander}, year={2008}, pages={462–464} }
 @article{young_nichols_kelly_deiters_2008, title={Microwave activation of enzymatic catalysis}, volume={130}, ISSN={["0002-7863"]}, DOI={10.1021/ja802404g}, abstractNote={Microwave irradiation can be used to regulate biocatalysis. Herein, the utilization of hyperthermophilic enzymes in a microwave reactor is reported. While these enzymes are inactive at low temperatures, they can be activated with microwave irradiation. To the best of our knowledge, this is the first illustration of a specific microwave effect in enzymatic catalysis.}, number={31}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Young, Douglas D. and Nichols, Jason and Kelly, Robert M. and Deiters, Alexander}, year={2008}, month={Aug}, pages={10048-+} }
 @article{young_torres-kolbus_deiters_2008, title={Microwave-assisted synthesis of unnatural amino acids}, volume={18}, ISSN={["0960-894X"]}, DOI={10.1016/j.bmcl.2008.09.025}, abstractNote={Microwave irradiation has been proven to be a useful tool in the rapid assembly of racemic unnatural amino acids in only two steps. Additional benefits of this methodology are the commercial availability of the inexpensive starting materials and the high yields and high purities of the final amino acid products.}, number={20}, journal={BIOORGANIC & MEDICINAL CHEMISTRY LETTERS}, author={Young, Douglas D. and Torres-Kolbus, Jessica and Deiters, Alexander}, year={2008}, month={Oct}, pages={5478–5480} }
 @article{teske_deiters_2008, title={Microwave-mediated Nickel-catalyzed cyclotrimerization reactions: Total synthesis of illudinine}, volume={73}, ISSN={["1520-6904"]}, DOI={10.1021/jo7020955}, abstractNote={Rapid and efficient [2 + 2 + 2] cyclotrimerization reactions were discovered through the application of microwave irradiation in conjunction with a Ni(CO)2(PPh3)2 catalyst. This enables the facile construction of highly substituted indane, isoindoline, and tetraline core structures. The developed microwave-mediated Ni-catalyzed cyclotrimerization reaction was employed as the key step in a concise synthesis of the isoquinoline natural product illudinine. This represents the first example of a Ni-catalyzed cyclotrimerization reaction in total synthesis.}, number={1}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Teske, Jesse A. and Deiters, Alexander}, year={2008}, month={Jan}, pages={342–345} }
 @article{sripada_teske_deiters_2008, title={Phenanthridine synthesis via [2+2+2] cyclotrimerization reactions}, volume={6}, ISSN={["1477-0520"]}, DOI={10.1039/b716519f}, abstractNote={A concise synthesis of phenanthridines via a microwave-assisted [2+2+2] cyclotrimerization reaction has been developed.}, number={2}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Sripada, Lakshminath and Teske, Jesse A. and Deiters, Alexander}, year={2008}, pages={263–265} }
 @article{gumireddy_young_xiong_hogenesch_huang_deiters_2008, title={Small-molecule inhibitors of microRNA miR-21 function}, volume={47}, ISSN={["1521-3773"]}, DOI={10.1002/anie.200801555}, abstractNote={Short, but significant, microRNAs (miRNAs) are an important class of gene regulators. Small-molecule modifiers of miRNA function, such as 1 (see schematic representation), were identified in a cellular screen for miRNA-pathway inhibitors. Such compounds are expected to be useful tools for the elucidation of detailed mechanisms of miRNA action and may serve as lead structures for the development of new therapeutic agents. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.}, number={39}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Gumireddy, Kiranmai and Young, Douglas D. and Xiong, Xin and Hogenesch, John B. and Huang, Qihong and Deiters, Alexander}, year={2008}, pages={7482–7484} }
 @article{lusic_gustilo_vendeix_kaiser_delaney_graham_moye_cantara_agris_deiters_2008, title={Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNA(Met)}, volume={36}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkn703}, abstractNote={Human mitochondrial methionine transfer RNA (hmtRNAMetCAU) has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position-34 (f5C34). The role of this modification in (hmtRNAMetCAU) for the decoding of AUA, as well as AUG, in both the peptidyl- and aminoacyl-sites of the ribosome in either chain initiation or chain elongation is still unknown. We report the first synthesis and analyses of the tRNA's anticodon stem and loop domain containing the 5-formylcytidine modification. The modification contributes to the tRNA's anticodon domain structure, thermodynamic properties and its ability to bind codons AUA and AUG in translational initiation and elongation.}, number={20}, journal={NUCLEIC ACIDS RESEARCH}, author={Lusic, Hrvoje and Gustilo, Estella M. and Vendeix, Franck A. P. and Kaiser, Rob and Delaney, Michael O. and Graham, William D. and Moye, Virginia A. and Cantara, William A. and Agris, Paul F. and Deiters, Alexander}, year={2008}, month={Nov}, pages={6548–6557} }
 @article{zou_young_cruz-montanez_deiters_2008, title={Synthesis of Anthracene and Azaanthracene Fluorophores via [2+2+2] Cyclotrimerization Reactions}, volume={10}, ISSN={["1523-7052"]}, DOI={10.1021/ol8019549}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVLetterNEXTSynthesis of Anthracene and Azaanthracene Fluorophores via [2+2+2] Cyclotrimerization ReactionsYan Zou†, Douglas D. Young†, Alejandra Cruz-Montanez, and Alexander Deiters*View Author Information Department of Chemistry, North Carolina State University, Campus Box 8204, Raleigh, North Carolina 27695-8204[email protected]†Both authors contributed equally to this work.Cite this: Org. Lett. 2008, 10, 20, 4661–4664Publication Date (Web):September 25, 2008Publication History Received20 August 2008Published online25 September 2008Published inissue 16 October 2008https://doi.org/10.1021/ol8019549Copyright © 2008 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2284Altmetric-Citations47LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (551 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Electromagnetic radiation,Fluorescence,Hydrocarbons,Solvents Get e-Alerts}, number={20}, journal={ORGANIC LETTERS}, author={Zou, Yan and Young, Douglas D. and Cruz-Montanez, Alejandra and Deiters, Alexander}, year={2008}, month={Oct}, pages={4661–4664} }
 @article{young_deiters_2007, title={A general approach to chemo- and regioselective cyclotrimerization reactions}, volume={46}, ISSN={["1433-7851"]}, DOI={10.1002/anie.200700802}, abstractNote={Microwave-ready heterocycles: Cobalt-catalyzed [2+2+2] cyclotrimerization of nitrile derivatives with diynes anchored to a solid support under microwave irradiation provides a universal approach to pyridine, pyridone, and iminopyridine products. The reaction is completely chemo- and regioselective, and the products are obtained in excellent yield and high purity.}, number={27}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Young, Douglas D. and Deiters, Alexander}, year={2007}, pages={5187–5190} }
 @article{young_sripada_deiters_2007, title={Microwave-assisted solid-supported alkyne cyclotrimerization reactions for combinatorial chemistry}, volume={9}, ISSN={["1520-4766"]}, DOI={10.1021/cc070068b}, abstractNote={ADVERTISEMENT RETURN TO ISSUEReportNEXTMicrowave-Assisted Solid-Supported Alkyne Cyclotrimerization Reactions for Combinatorial ChemistryDouglas D. Young, Lakshminath Sripada, and Alexander DeitersView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204 Cite this: J. Comb. Chem. 2007, 9, 5, 735–738Publication Date (Web):July 21, 2007Publication History Received4 May 2007Published online21 July 2007Published inissue 1 September 2007https://doi.org/10.1021/cc070068bCopyright © 2007 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views723Altmetric-Citations35LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (243 KB) Supporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Electromagnetic radiation,Hydrocarbons,Irradiation,Reactivity Get e-Alerts}, number={5}, journal={JOURNAL OF COMBINATORIAL CHEMISTRY}, author={Young, Douglas D. and Sripada, Lakshminath and Deiters, Alexander}, year={2007}, pages={735–738} }
 @article{lusic_young_lively_deiters_2007, title={Photochemical DNA activation}, volume={9}, ISSN={["1523-7052"]}, DOI={10.1021/ol070455u}, abstractNote={A new photocaged nucleoside was synthesized and incorporated into DNA with the use of standard synthesis conditions. This approach enabled the disruption of specific H-bonds and allowed for the analysis of their contribution to the activity of a DNAzyme. Brief irradiation with nonphotodamaging UV light led to rapid decaging and almost quantitative restoration of DNAzyme activity. The developed strategy has the potential to find widespread application in the light-induced regulation of oligonucleotide function.}, number={10}, journal={ORGANIC LETTERS}, author={Lusic, Hrvoje and Young, Douglas D. and Lively, Mark O. and Deiters, Alexander}, year={2007}, month={May}, pages={1903–1906} }
 @article{young_deiters_2007, title={Photochemical activation of protein expression in bacterial cells}, volume={46}, ISSN={["1521-3773"]}, DOI={10.1002/anie.200700057}, abstractNote={Turning genes on with light: Photochemical control of gene expression is a versatile tool for the elucidation of biological processes and the programming of new biological functions. Activation of protein expression in prokaryotic cells through light irradiation is achieved through a photocaged small molecule. Spatiotemporal regulation of the lac operon was obtained through the application of a photocaged isopropyl-β-D-thiogalactopyranoside derivative.}, number={23}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Young, Douglas D. and Deiters, Alexander}, year={2007}, pages={4290–4292} }
 @article{young_deiters_2007, title={Photochemical control of biological processes}, volume={5}, ISSN={["1477-0539"]}, DOI={10.1039/b616410m}, abstractNote={Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.}, number={7}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Young, Douglas D. and Deiters, Alexander}, year={2007}, pages={999–1005} }
 @article{senaiar_teske_young_deiters_2007, title={Synthesis of indanones via solid-supported [2+2+2] cyclotrimerization}, volume={72}, ISSN={["0022-3263"]}, DOI={10.1021/jo7013565}, abstractNote={A new facile approach toward natural and unnatural indanones has been developed, featuring a solid-supported [2+2+2] cyclotrimerization as the key step. This strategy has been applied to the chemo- and regioselective assembly of indanone arrays and to the total synthesis of a recently isolated indanone marine natural product.}, number={20}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Senaiar, Ramesh S. and Teske, Jesse A. and Young, Douglas D. and Deiters, Alexander}, year={2007}, month={Sep}, pages={7801–7804} }
 @article{summerer_chen_wu_deiters_chin_schultz_2006, title={A genetically encoded fluorescent amino acid}, volume={103}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0603965103}, abstractNote={The ability to introduce fluorophores selectively into proteins provides a powerful tool to study protein structure, dynamics, localization, and biomolecular interactions both in vitro and in vivo . Here, we report a strategy for the selective and efficient biosynthetic incorporation of a low-molecular-weight fluorophore into proteins at defined sites. The fluorescent amino acid 2-amino-3-(5-(dimethylamino)naphthalene-1-sulfonamide)propanoic acid (dansylalanine) was genetically encoded in Saccharomyces cerevisiae by using an amber nonsense codon and corresponding orthogonal tRNA/aminoacyl-tRNA synthetase pair. This environmentally sensitive fluorophore was selectively introduced into human superoxide dismutase and used to monitor unfolding of the protein in the presence of guanidinium chloride. The strategy described here should be applicable to a number of different fluorophores in both prokaryotic and eukaryotic organisms, and it should facilitate both biochemical and cellular studies of protein structure and function.}, number={26}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Summerer, Daniel and Chen, Shuo and Wu, Ning and Deiters, Alexander and Chin, Jason W. and Schultz, Peter G.}, year={2006}, month={Jun}, pages={9785–9789} }
 @article{deiters_groff_ryu_xie_schultz_2006, title={A genetically encoded photocaged tyrosine}, volume={45}, ISSN={["1521-3773"]}, DOI={10.1002/anie.200600264}, abstractNote={Activating proteins with light: A photocaged tyrosine was genetically encoded in E. coli in response to the amber codon TAG. Substitution of Tyr 503 in the active site of β-galactosidase allowed photoactivation of this enzyme in vitro or directly in bacteria with 360-nm light. This method should allow photoregulation of the activity of a variety of biological processes including transcription, signal transduction, and cellular trafficking.}, number={17}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Deiters, A and Groff, D and Ryu, YH and Xie, JM and Schultz, PG}, year={2006}, pages={2728–2731} }
 @article{lusic_deiters_2006, title={A new photocaging group for aromatic N-heterocycles}, ISSN={["1437-210X"]}, DOI={10.1055/s-2006-942424}, abstractNote={Biologically relevant nitrogen-containing heterocycles were photo-protected using an NPOM caging group that is stable under physiological conditions but readily decages under irradiation with non-photodamaging UV light.}, number={13}, journal={SYNTHESIS-STUTTGART}, author={Lusic, Hrvoje and Deiters, Alexander}, year={2006}, month={Jul}, pages={2147–2150} }
 @article{deiters_yoder_2006, title={Conditional transgene and gene targeting methodologies in zebrafish}, volume={3}, journal={Zebrafish}, author={Deiters, A. and Yoder, J. A.}, year={2006}, pages={415–429} }
 @misc{deiters_pettersson_martin_2006, title={General strategy for the syntheses of corynanthe, tacaman, and oxindole alkaloids}, volume={71}, ISSN={["1520-6904"]}, DOI={10.1021/jo061032t}, abstractNote={We report herein the total synthesis of the corynanthe alkaloid dihydrocorynantheol and the formal syntheses of the indole alkaloids tacamonine, rhynchophylline, and hirsutine. The strategies for assembling the corynanthe and tacaman skeletal frameworks comprised of both the classical ABD --> ABCD and ABC --> ABCD approaches wherein the variously substituted piperidinone D-rings were formed via ring-closing metathesis (RCM) followed by a 1,4-addition to introduce the requisite side chain at C(15). Since 1,4-additions to alpha,beta-unsaturated lactams represent an underdeveloped field, we conducted a series of studies with two unsaturated lactams employing organocuprates and metal enolates as the nucleophiles. These studies revealed that organocuprates derived from Grignard reagents and either stoichiometric amounts of CuCN or catalytic amounts of CuBr.DMS complex are excellent nucleophiles for such additions; TMSCl was a crucial additive for optimizing these reactions. The anion derived from ethyl 1,3-dithiolane-2-carboxylate was also an excellent nucleophile in these 1,4-additions, although the stereochemistry of such 1,4-additions to carboline-derived, unsaturated lactams was sensitive to substitution on the indole nitrogen atom. The ABD --> ABCD approach to these alkaloids featured a novel one-pot sequence of an RCM reaction and a zirconocene-catalyzed carbomagnesation followed by a second RCM to generate the D-ring.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Deiters, Alexander and Pettersson, Martin and Martin, Stephen F.}, year={2006}, month={Aug}, pages={6547–6561} }
 @article{young_deiters_2006, title={Photochemical hammerhead ribozyme activation}, volume={16}, ISSN={["1464-3405"]}, DOI={10.1016/j.bmcl.2006.02.034}, abstractNote={We report the light-activation of allosteric cis and trans acting ribozymes via decaging of a small organic molecule ligand. To achieve this effectively, we introduce an optimized N-caging group based on a nitrobenzyl core structure. This approach can potentially be employed toward a light-induced control of gene function.}, number={10}, journal={BIOORGANIC & MEDICINAL CHEMISTRY LETTERS}, author={Young, DD and Deiters, A}, year={2006}, month={May}, pages={2658–2661} }
 @article{senaiar_young_deiters_2006, title={Pyridines via solid-supported [2+2+2] cyclotrimerization}, DOI={10.1039/b515901f}, abstractNote={The formation of pyridines via a crossed [2 + 2 + 2] cycloaddition has been achieved on a solid-support for the first time.}, number={12}, journal={Chemical Communications (Cambridge, England)}, author={Senaiar, R. S. and Young, D. D. and Deiters, A.}, year={2006}, pages={1313–1315} }
 @article{young_senaiar_deiters_2006, title={Solid-supported [2+2+2] cyclotrimerizations}, volume={12}, ISSN={["0947-6539"]}, DOI={10.1002/chem.200501360}, abstractNote={The transition-metal-catalyzed [2+2+2] cyclotrimerization of a diyne and an alkyne provides a convergent route to highly-substituted aromatic rings. This reaction possesses distinct drawbacks, especially low chemo- and regioselectivities, which hamper its application in combinatorial synthesis. These problems have been solved by the development of solid-supported [2+2+2]-cycloaddition reactions. If conducted on a solid-support, this reaction enables rapid combinatorial access to diverse sets of carbo- and heterocyclic small-molecule arrays. The scope of this methodology has been investigated by examining different immobilization strategies, different diyne precursors, and a variety of functionalized alkyne reaction partners. Overall, isoindoline, phthalan, and indan libraries were assembled in good to excellent yields and with high purities.}, number={21}, journal={CHEMISTRY-A EUROPEAN JOURNAL}, author={Young, Douglas D. and Senaiar, Ramesh S. and Deiters, Alexander}, year={2006}, month={Jul}, pages={5563–5568} }
 @misc{deiters_martin_2004, title={Synthesis of oxygen- and nitrogen-containing heterocycles by ring-closing metathesis}, volume={104}, ISSN={["1520-6890"]}, DOI={10.1021/cr0200872}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Oxygen- and Nitrogen-Containing Heterocycles by Ring-Closing MetathesisAlexander Deiters and Stephen F. MartinView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, and Department of Chemistry and Biochemistry, The University of Texas, Austin, Texas 78712 Cite this: Chem. Rev. 2004, 104, 5, 2199–2238Publication Date (Web):April 27, 2004Publication History Received16 October 2003Published online27 April 2004Published inissue 1 May 2004https://doi.org/10.1021/cr0200872Copyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views12619Altmetric-Citations1164LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (1 MB) Get e-AlertsSUBJECTS:Catalysts,Cyclization,Ethers,Lactones,Metathesis Get e-Alerts}, number={5}, journal={CHEMICAL REVIEWS}, author={Deiters, A and Martin, SF}, year={2004}, month={May}, pages={2199–2238} }