@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{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{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{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, hmtRNA(Met)(CAU), to read AUG and AUA codons at both the peptidyl- (P-), and aminoacyl- (A-) sites of the ribosome. The hmtRNA(Met)(CAU) has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position 34 (f(5)C(34)), 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 (hmtASL(Met)(CAU)), determined by NMR restrained molecular modeling, revealed how the f(5)C(34) modification facilitates the decoding of AUA at the P- and the A-sites. The f(5)C(34) defined a reduced conformational space for the nucleoside, in what appears to have restricted the conformational dynamics of the anticodon bases of the modified hmtASL(Met)(CAU). The hmtASL(Met)(CAU) 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 f(5)C(34) 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 f(5)C(34) enabled P-site codon binding to these normally isoleucine codons. Thus, the physicochemical properties of this one modification, f(5)C(34), 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{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 ((19)F-UAAs). We then increased the permissivity of the initial UaaRSs to allow for incorporation of the family of (19)F-UAAs. Finally, we validated the utility of these new (19)F-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{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{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-+} }
 @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{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={Detailed knowledge of the external regulation of gene func-tion is a fundamental necessity in order to annotate sequencedgenomes and to understand biological processes in single cellsand multicellular organisms. One of the most widely used ap-proaches for the down-regulation of specific genes is the ap-plication of antisense agents. Antisense agents are oligomersthat have the ability to hybridize sequence specificslly tomRNAs, inhibiting translation and potentially leading to mRNAdegradation through RNAse H recruitment.}, 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_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{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{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{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} }