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dc.contributor.authorNguyen, Kimspa
dc.contributor.authorKubota, Milesspa
dc.contributor.authorDel Arco, Jonspa
dc.contributor.authorFeng, Chaospa
dc.contributor.authorSingha, Monikaspa
dc.contributor.authorBeasley, Samanthaspa
dc.contributor.authorSakr, Jasminespa
dc.contributor.authorP. Gandhi, Sunilspa
dc.contributor.authorBlurton-Jones, Mathewspa
dc.contributor.authorFernández Lucas, Jesusspa
dc.contributor.authorC. Spitale, Robertspa
dc.description.abstractProfiling RNA expression in a cell-specific manner continues to be a grand challenge in biochemical research. Bioorthogonal nucleosides can be utilized to track RNA expression; however, these methods currently have limitations due to background and incorporation of analogs into undesired cells. Herein, we design and demonstrate that uracil phosphoribosyltransferase can be engineered to match 5-vinyluracil for cell-specific metabolic labeling of RNA with exceptional specificity and
dc.publisherCorporación Universidad de la Costaspa
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internationalspa
dc.sourceACS Chemical Biologyspa
dc.subjectPeptides and proteinsspa
dc.subjectImaging probesspa
dc.titleA bump-hole strategy for increased stringency of cell-specific metabolic labeling of rnaspa
dc.typeArtículo de revistaspa
dc.identifier.instnameCorporación Universidad de la Costaspa
dc.identifier.reponameREDICUC - Repositorio CUCspa
dc.relation.referencesLandgraf, P., Antileo, E. R., Schuman, E. M., and Dieterich, D. C. (2015) BONCAT: metabolic labeling, click chemistry, and affinity purification of newly synthesized proteomes. Methods Mol. Biol. 1266, 199– 215, DOI: 10.1007/978-1-4939-2272-7_14spa
dc.relation.referencesKrogager, T. P., Ernst, R. J., Elliott, T. S., Calo, L., Beranek, V., Ciabatti, E., Spillantini, M. G., Tripodi, M., Hastings, M. H., and Chin, J. W. (2018) Labeling and identifying cell-specific proteomes in the mouse brain. Nat. Biotechnol. 36 (2), 156– 159, DOI: 10.1038/nbt.4056spa
dc.relation.referencesErnst, R. J., Krogager, T. P., Maywood, E. S., Zanchi, R., Beranek, V., Elliott, T. S., Barry, N. P., Hastings, M. H., and Chin, J. W. (2016) Genetic code expansion in the mouse brain. Nat. Chem. Biol. 12 (10), 776– 778, DOI: 10.1038/nchembio.2160spa
dc.relation.referencesBarrett, R. M., Liu, H. W., Jin, H., Goodman, R. H., and Cohen, M. S. (2016) Cell-specific Profiling of Nascent Proteomes Using Orthogonal Enzyme-mediated Puromycin Incorporation. ACS Chem. Biol. 11 (6), 1532– 6, DOI: 10.1021/acschembio.5b01076spa
dc.relation.referencesLi, Z., Zhu, Y., Sun, Y., Qin, K., Liu, W., Zhou, W., and Chen, X. (2016) Nitrilase-Activatable Noncanonical Amino Acid Precursors for Cell-Selective Metabolic Labeling of Proteomes. ACS Chem. Biol. 11 (12), 3273– 3277, DOI: 10.1021/acschembio.6b00765spa
dc.relation.referencesTriemer, T., Messikommer, A., Glasauer, S. M. K., Alzeer, J., Paulisch, M. H., and Luedtke, N. W. (2018) Superresolution imaging of individual replication forks reveals unexpected prodrug resistance mechanism. Proc. Natl. Acad. Sci. U. S. A. 115 (7), E1366– E1373, DOI: 10.1073/pnas.1714790115spa
dc.relation.referencesNeef, A. B., Pernot, L., Schreier, V. N., Scapozza, L., and Luedtke, N. W. (2015) A Bioorthogonal Chemical Reporter of Viral Infection. Angew. Chem. 127 (27), 8022– 8025, DOI: 10.1002/ange.201500250spa
dc.relation.referencesHubbard, S. C., Boyce, M., McVaugh, C. T., Peehl, D. M., and Bertozzi, C. R. (2011) Cell surface glycoproteomic analysis of prostate cancer-derived PC-3 cells. Bioorg. Med. Chem. Lett. 21 (17), 4945– 50, DOI: 10.1016/j.bmcl.2011.05.045spa
dc.relation.referencesRabuka, D., Forstner, M. B., Groves, J. T., and Bertozzi, C. R. (2008) Noncovalent cell surface engineering: incorporation of bioactive synthetic glycopolymers into cellular membranes. J. Am. Chem. Soc. 130 (18), 5947– 53, DOI: 10.1021/ja710644gspa
dc.relation.referencesChang, P. V., Prescher, J. A., Hangauer, M. J., and Bertozzi, C. R. (2007) Imaging cell surface glycans with bioorthogonal chemical reporters. J. Am. Chem. Soc. 129 (27), 8400– 1, DOI: 10.1021/ja070238ospa
dc.relation.referencesJao, C. Y. and Salic, A. (2008) Exploring RNA transcription and turnover in vivo by using click chemistry. Proc. Natl. Acad. Sci. U. S. A. 105 (41), 15779– 84, DOI: 10.1073/pnas.0808480105spa
dc.relation.referencesZheng, Y. and Beal, P. A. (2016) Synthesis and evaluation of an alkyne-modified ATP analog for enzymatic incorporation into RNA. Bioorg. Med. Chem. Lett. 26 (7), 1799– 802, DOI: 10.1016/j.bmcl.2016.02.038spa
dc.relation.referencesNainar, S., Beasley, S., Fazio, M., Kubota, M., Dai, N., Correa, I. R., Jr., and Spitale, R. C. (2016) Metabolic Incorporation of Azide Functionality into Cellular RNA. ChemBioChem 17 (22), 2149– 2152, DOI: 10.1002/cbic.201600300spa
dc.relation.referencesHida, N., Aboukilila, M. Y., Burow, D. A., Paul, R., Greenberg, M. M., Fazio, M., Beasley, S., Spitale, R. C., and Cleary, M. D. (2017) EC-tagging allows cell type-specific RNA analysis. Nucleic Acids Res. 45 (15), e138 DOI: 10.1093/nar/gkx551spa
dc.relation.referencesAbud, E. M., Ramirez, R. N., Martinez, E. S., Healy, L. M., Nguyen, C. H. H., Newman, S. A., Yeromin, A. V., Scarfone, V. M., Marsh, S. E., Fimbres, C., Caraway, C. A., Fote, G. M., Madany, A. M., Agrawal, A., Kayed, R., Gylys, K. H., Cahalan, M. D., Cummings, B. J., Antel, J. P., Mortazavi, A., Carson, M. J., Poon, W. W., and Blurton-Jones, M. (2017) iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases. Neuron 94 (2), 278– 293, DOI: 10.1016/j.neuron.2017.03.042spa
dc.relation.referencesIslam, K. (2018) The Bump-and-Hole Tactic: Expanding the Scope of Chemical Genetics. Cell Chem. Biol. 25 (10), 1171– 1184, DOI: 10.1016/j.chembiol.2018.07.001spa
dc.relation.referencesYu, H., Li, J., Wu, D., Qiu, Z., and Zhang, Y. (2010) Chemistry and biological applications of photo-labile organic molecules. Chem. Soc. Rev. 39 (2), 464– 73, DOI: 10.1039/B901255Aspa
dc.relation.referencesNainar, S., Cuthbert, B. J., Lim, N. M., England, W. E., Ke, K., Sophal, K., Quechol, R., Mobley, D. L., Goulding, C. W., and Spitale, R. C. (2020) An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. Nat. Methods 17 (3), 311– 318, DOI: 10.1038/s41592-019-0726-yspa
dc.relation.referencesWang, D., Zhang, Y., and Kleiner, R. E. (2020) Cell- and Polymerase-Selective Metabolic Labeling of Cellular RNA with 2’-Azidocytidine. J. Am. Chem. Soc. 142 (34), 14417– 14421, DOI: 10.1021/jacs.0c04566spa
dc.relation.referencesZhang, Y. and Kleiner, R. E. (2019) A Metabolic Engineering Approach to Incorporate Modified Pyrimidine Nucleosides into Cellular RNA. J. Am. Chem. Soc. 141 (8), 3347– 3351, DOI: 10.1021/jacs.8b11449spa
dc.relation.referencesXie, R., Dong, L., Du, Y., Zhu, Y., Hua, R., Zhang, C., and Chen, X. (2016) In vivo metabolic labeling of sialoglycans in the mouse brain by using a liposome-assisted bioorthogonal reporter strategy. Proc. Natl. Acad. Sci. U. S. A. 113 (19), 5173– 8, DOI: 10.1073/pnas.1516524113spa
dc.relation.referencesVinogradov, S. V. (2007) Polymeric nanogel formulations of nucleoside analogs. Expert Opin. Drug Delivery 4 (1), 5– 17, DOI: 10.1517/17425247.4.1.5spa
dc.relation.referencesBalimane, P. V. and Sinko, P. J. (1999) Involvement of multiple transporters in the oral absorption of nucleoside analogues. Adv. Drug Delivery Rev. 39 (1–3), 183– 209, DOI: 10.1016/S0169-409X(99)00026-5spa
dc.relation.referencesTomorsky, J., DeBlander, L., Kentros, C. G., Doe, C. Q., and Niell, C. M. (2017) TU-Tagging: A Method for Identifying Layer-Enriched Neuronal Genes in Developing Mouse Visual Cortex. eNeuro 4 (5), ENEURO.0181-17.2017, DOI: 10.1523/ENEURO.0181-17.2017spa
dc.relation.referencesGay, L., Miller, M. R., Ventura, P. B., Devasthali, V., Vue, Z., Thompson, H. L., Temple, S., Zong, H., Cleary, M. D., Stankunas, K., and Doe, C. Q. (2013) Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA. Genes Dev. 27 (1), 98– 115, DOI: 10.1101/gad.205278.112spa
dc.relation.referencesBasnet, H., Tian, L., Ganesh, K., Huang, Y. H., Macalinao, D. G., Brogi, E., Finley, L. W., and Massague, J. (2019) Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization. eLife 8, e43627 DOI: 10.7554/eLife.43627spa
dc.relation.referencesNguyen, K., Fazio, M., Kubota, M., Nainar, S., Feng, C., Li, X., Atwood, S. X., Bredy, T. W., and Spitale, R. C. (2017) Cell-Selective Bioorthogonal Metabolic Labeling of RNA. J. Am. Chem. Soc. 139 (6), 2148– 2151, DOI: 10.1021/jacs.6b11401spa
dc.relation.referencesKubota, M., Nainar, S., Parker, S. M., England, W., Furche, F., and Spitale, R. C. (2019) Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry. ACS Chem. Biol. 14 (8), 1698– 1707, DOI: 10.1021/acschembio.9b00079spa
dc.relation.referencesRieder, U. and Luedtke, N. W. (2014) Alkene-tetrazine ligation for imaging cellular DNA. Angew. Chem., Int. Ed. 53 (35), 9168– 72, DOI: 10.1002/anie.201403580spa
dc.relation.referencesKnall, A. C. and Slugovc, C. (2013) Inverse electron demand Diels-Alder (iEDDA)-initiated conjugation: a (high) potential click chemistry scheme. Chem. Soc. Rev. 42 (12), 5131– 42, DOI: 10.1039/c3cs60049aspa

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Attribution-NonCommercial-NoDerivatives 4.0 International
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