@article{luo_arbely_zhang_chou_uprety_chin_deiters_2016, title={Genetically encoded optical activation of DNA recombination in human cells}, volume={52}, ISSN={["1364-548X"]}, DOI={10.1039/c6cc03934k}, abstractNote={Two precisely regulated, light-activated Cre recombinase enzymes were generated through the site-specific incorporation of two genetically encoded photocaged amino acids in human cells.}, number={55}, journal={CHEMICAL COMMUNICATIONS}, author={Luo, J. and Arbely, E. and Zhang, J. and Chou, C. and Uprety, R. and Chin, J. W. and Deiters, A.}, year={2016}, pages={8529–8532} }
 @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{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={AbstractWe 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{luo_uprety_naro_chou_nguyen_chin_deiters_2014, title={Genetically Encoded Optochemical Probes for Simultaneous Fluorescence Reporting and Light Activation of Protein Function with Two-Photon Excitation}, volume={136}, ISSN={["1520-5126"]}, DOI={10.1021/ja5055862}, abstractNote={The site-specific incorporation of three new coumarin lysine analogues into proteins was achieved in bacterial and mammalian cells using an engineered pyrrolysyl-tRNA synthetase system. The genetically encoded coumarin lysines were successfully applied as fluorescent cellular probes for protein localization and for the optical activation of protein function. As a proof-of-principle, photoregulation of firefly luciferase was achieved in live cells by caging a key lysine residue, and excellent OFF to ON light-switching ratios were observed. Furthermore, two-photon and single-photon optochemical control of EGFP maturation was demonstrated, enabling the use of different, potentially orthogonal excitation wavelengths (365, 405, and 760 nm) for the sequential activation of protein function in live cells. These results demonstrate that coumarin lysines are a new and valuable class of optical probes that can be used for the investigation and regulation of protein structure, dynamics, function, and localization in live cells. The small size of coumarin, the site-specific incorporation, the application as both a light-activated caging group and as a fluorescent probe, and the broad range of excitation wavelengths are advantageous over other genetically encoded photocontrol systems and provide a precise and multifunctional tool for cellular biology.}, number={44}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Luo, Ji and Uprety, Rajendra and Naro, Yuta and Chou, Chungjung and Nguyen, Duy P. and Chin, Jason W. and Deiters, Alexander}, year={2014}, month={Nov}, pages={15551–15558} }
 @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_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{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{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{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} }