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Jason R. Stagno, Ph.D. - Publications

Affiliations: 
2009 University of California, Irvine, Irvine, CA 
Area:
Biochemistry, Molecular Biology
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Ding J, Deme JC, Stagno JR, Yu P, Lea SM, Wang YX. Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM. Nucleic Acids Research. PMID 37534568 DOI: 10.1093/nar/gkad651  0.38
2023 Wang YX, Degenhardt M, Degenhardt H, Bhandari Y, Lee YT, Ding J, Heinz W, Stagno J, Schwieters C, Zhang J. Determining structures of individual RNA conformers using atomic force microscopy images and deep neural networks. Research Square. PMID 37425706 DOI: 10.21203/rs.3.rs-2798658/v1  0.326
2023 Lee HK, Lee YT, Fan L, Wilt HM, Conrad CE, Yu P, Zhang J, Shi G, Ji X, Wang YX, Stagno JR. Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state. Structure (London, England : 1993). PMID 37253356 DOI: 10.1016/j.str.2023.05.003  0.322
2023 Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX. Visualizing RNA conformational and architectural heterogeneity in solution. Nature Communications. 14: 714. PMID 36759615 DOI: 10.1038/s41467-023-36184-x  0.51
2022 Stagno JR, Knoska J, Chapman HN, Wang YX. Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates. Methods in Molecular Biology (Clifton, N.J.). 2568: 243-249. PMID 36227573 DOI: 10.1007/978-1-0716-2687-0_16  0.401
2022 Stagno JR. Preparation of RNA Microcrystals for Serial Femtosecond Crystallography Experiments. Methods in Molecular Biology (Clifton, N.J.). 2568: 233-242. PMID 36227572 DOI: 10.1007/978-1-0716-2687-0_15  0.427
2021 Ramakrishnan S, Stagno JR, Conrad CE, Ding J, Yu P, Bhandari YR, Lee YT, Pauly G, Yefanov O, Wiedorn MO, Knoska J, Oberthür D, White TA, Barty A, Mariani V, et al. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nature Communications. 12: 1762. PMID 33741910 DOI: 10.1038/s41467-021-21838-5  0.316
2019 Ding J, Swain M, Yu P, Stagno JR, Wang YX. Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser. Journal of Biomolecular Nmr. PMID 31606878 DOI: 10.1007/S10858-019-00278-W  0.332
2019 Trachman RJ, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferré-D'Amaré AR. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Crystallographica. Section F, Structural Biology Communications. 75: 547-551. PMID 31397326 DOI: 10.1107/S2053230X19010136  0.402
2019 Jones C, Tran B, Conrad C, Stagno J, Trachman R, Fischer P, Meents A, Ferré-D'Amaré A. Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser. Acta Crystallographica. Section F, Structural Biology Communications. 75: 496-500. PMID 31282869 DOI: 10.1107/S2053230X19008549  0.316
2019 Stagno JR, Yu P, Dyba MA, Wang YX, Liu Y. Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing. Plos One. 14: e0215555. PMID 30986270 DOI: 10.1371/journal.pone.0215555  0.543
2019 Stagno JR, Yu P, Spinale A, Todd PW, Giulianotti M, Wang Y. Effects of microgravity crystallization on a ligand-induced RNA crystal phase transition Acta Crystallographica Section a Foundations and Advances. 75: a128-a128. DOI: 10.1107/s0108767319098714  0.337
2018 Liu Y, Holmstrom E, Yu P, Tan K, Zuo X, Nesbitt DJ, Sousa R, Stagno JR, Wang YX. Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA. Nature Protocols. 13: 987-1005. PMID 29651055 DOI: 10.1038/Nprot.2018.002  0.515
2017 Bhandari YR, Fan L, Fang X, Zaki G, Stahlberg EA, Jiang W, Schwieters CD, Stagno JR, Wang YX. Topological structure determination of RNA using small angle X-ray scattering. Journal of Molecular Biology. PMID 28918093 DOI: 10.1016/J.Jmb.2017.09.006  0.582
2017 Stagno JR, Bhandari YR, Conrad CE, Liu Y, Wang YX. Real-time crystallographic studies of the adenine riboswitch using an X-ray free electron laser. The Febs Journal. PMID 28504865 DOI: 10.1111/Febs.14110  0.316
2017 Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, et al. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography Acta Crystallographica Section a Foundations and Advances. 73: a92-a92. DOI: 10.1107/S0108767317099081  0.472
2017 van Beek H, Handing K, Gualtier E, Stagno J, Wang Y, Ramsey L. Sensitive detection of RNA microcrystals using SONICC imaging Acta Crystallographica Section a Foundations and Advances. 73: a201-a201. DOI: 10.1107/S0108767317098026  0.374
2016 Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, et al. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature. PMID 27841871 DOI: 10.1038/Nature20599  0.446
2016 Rajappa-Titu L, Suematsu T, Munoz-Tello P, Long M, Demir Ö, Cheng KJ, Stagno JR, Luecke H, Amaro RE, Aphasizheva I, Aphasizhev R, Thore S. RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting. Nucleic Acids Research. PMID 27744351 DOI: 10.1093/Nar/Gkw917  0.685
2016 Bhandari YR, Jiang W, Stahlberg EA, Stagno JR, Wang YX. Modeling RNA Topological Structures Using Small Angle X-Ray Scattering. Methods (San Diego, Calif.). PMID 27090001 DOI: 10.1016/J.Ymeth.2016.04.015  0.535
2016 Liu Y, Yu P, Dyba M, Sousa R, Stagno JR, Wang YX. Applications of PLOR in labeling large RNAs at specific sites. Methods (San Diego, Calif.). PMID 27033177 DOI: 10.1016/J.Ymeth.2016.03.014  0.52
2015 Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba MA, Chen D, Ying J, Lockett S, Nesbitt DJ, Ferré-D'Amaré AR, Sousa R, Stagno JR, Wang YX. Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature. 522: 368-72. PMID 25938715 DOI: 10.1038/Nature14352  0.52
2015 Fang X, Stagno JR, Bhandari YR, Zuo X, Wang YX. Small-angle X-ray scattering: A bridge between RNA secondary structures and three-dimensional topological structures Current Opinion in Structural Biology. 30: 147-160. PMID 25765781 DOI: 10.1016/J.Sbi.2015.02.010  0.516
2012 Stagno JR, Ma B, Li J, Altieri AS, Byrd RA, Ji X. Crystal structure of a plectonemic RNA supercoil. Nature Communications. 3: 901. PMID 22692544 DOI: 10.1038/Ncomms1903  0.609
2011 Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, Byrd RA, Ji X. Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination. Nucleic Acids Research. 39: 7803-15. PMID 21652641 DOI: 10.1093/Nar/Gkr418  0.635
2010 Ringpis G, Stagno J, Aphasizhev R. Mechanism of U-insertion RNA editing in trypanosome mitochondria: characterization of RET2 functional domains by mutational analysis. Journal of Molecular Biology. 399: 696-706. PMID 20417643 DOI: 10.1016/J.Jmb.2010.04.035  0.71
2010 Stagno J, Aphasizheva I, Bruystens J, Luecke H, Aphasizhev R. Structure of the mitochondrial editosome-like complex associated TUTase 1 reveals divergent mechanisms of UTP selection and domain organization. Journal of Molecular Biology. 399: 464-75. PMID 20403364 DOI: 10.1016/J.Jmb.2010.04.021  0.693
2008 Luecke H, Schobert B, Stagno J, Imasheva ES, Wang JM, Balashov SP, Lanyi JK. Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proceedings of the National Academy of Sciences of the United States of America. 105: 16561-5. PMID 18922772 DOI: 10.1073/Pnas.0807162105  0.529
2007 Stagno J, Aphasizheva I, Aphasizhev R, Luecke H. Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases. Proceedings of the National Academy of Sciences of the United States of America. 104: 14634-9. PMID 17785418 DOI: 10.1073/Pnas.0704259104  0.688
2007 Garvie CW, Stagno JR, Reid S, Singh A, Harrington E, Boss JM. Characterization of the RFX complex and the RFX5(L66A) mutant: implications for the regulation of MHC class II gene expression. Biochemistry. 46: 1597-611. PMID 17279624 DOI: 10.1021/Bi6023868  0.378
2007 Stagno J, Aphasizheva I, Rosengarth A, Luecke H, Aphasizhev R. UTP-bound and Apo structures of a minimal RNA uridylyltransferase. Journal of Molecular Biology. 366: 882-99. PMID 17189640 DOI: 10.1016/J.Jmb.2006.11.065  0.701
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