Joseph Puglisi - Publications

Affiliations: 
Structural Biology Stanford University School of Medicine, Palo Alto, CA, United States 
Area:
the role of RNA in cellular processes and disease
Website:
http://puglisi.stanford.edu/

153 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
2020 Johnson AG, Flynn RA, Lapointe CP, Ooi YS, Zhao ML, Richards CM, Qiao W, Yamada SB, Couthouis J, Gitler AD, Carette JE, Puglisi JD. A memory of eS25 loss drives resistance phenotypes. Nucleic Acids Research. PMID 32463448 DOI: 10.1093/nar/gkaa444  0.4
2020 Choi J, O'Loughlin S, Atkins JF, Puglisi JD. The energy landscape of -1 ribosomal frameshifting. Science Advances. 6: eaax6969. PMID 31911945 DOI: 10.1126/sciadv.aax6969  0.4
2019 Verma M, Choi J, Cottrell KA, Lavagnino Z, Thomas EN, Pavlovic-Djuranovic S, Szczesny P, Piston DW, Zaher HS, Puglisi JD, Djuranovic S. A short translational ramp determines the efficiency of protein synthesis. Nature Communications. 10: 5774. PMID 31852903 DOI: 10.1038/s41467-019-13810-1  0.4
2019 Choi J, Marks J, Zhang J, Chen DH, Wang J, Vázquez-Laslop N, Mankin AS, Puglisi JD. Dynamics of the context-specific translation arrest by chloramphenicol and linezolid. Nature Chemical Biology. PMID 31844301 DOI: 10.1038/s41589-019-0423-2  0.4
2019 Chandrasekaran V, Juszkiewicz S, Choi J, Puglisi JD, Brown A, Shao S, Ramakrishnan V, Hegde RS. Mechanism of ribosome stalling during translation of a poly(A) tail. Nature Structural & Molecular Biology. PMID 31768042 DOI: 10.1038/s41594-019-0331-x  0.4
2019 Duss O, Stepanyuk GA, Puglisi JD, Williamson JR. Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding. Cell. 179: 1357-1369.e16. PMID 31761533 DOI: 10.1016/j.cell.2019.10.035  0.96
2019 Wang J, Johnson AG, Lapointe CP, Choi J, Prabhakar A, Chen DH, Petrov AN, Puglisi JD. eIF5B gates the transition from translation initiation to elongation. Nature. PMID 31534220 DOI: 10.1038/s41586-019-1561-0  0.4
2019 Yamada SB, Gendron TF, Niccoli T, Genuth NR, Grosely R, Shi Y, Glaria I, Kramer NJ, Nakayama L, Fang S, Dinger TJI, Thoeng A, Rocha G, Barna M, Puglisi JD, et al. RPS25 is required for efficient RAN translation of C9orf72 and other neurodegenerative disease-associated nucleotide repeats. Nature Neuroscience. PMID 31358992 DOI: 10.1038/s41593-019-0455-7  0.4
2019 Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD. Relating Structure and Dynamics in RNA Biology. Cold Spring Harbor Perspectives in Biology. 11. PMID 31262948 DOI: 10.1101/cshperspect.a032474  0.4
2019 Choi J, Grosely R, Puglisi EV, Puglisi JD. Expanding single-molecule fluorescence spectroscopy to capture complexity in biology. Current Opinion in Structural Biology. PMID 31213390 DOI: 10.1016/j.sbi.2019.05.005  0.4
2019 Johnson AG, Lapointe CP, Wang J, Corsepius NC, Choi J, Fuchs G, Puglisi JD. RACK1 on and off the ribosome. Rna (New York, N.Y.). PMID 31023766 DOI: 10.1261/rna.071217.119  0.4
2018 Duss O, Stepanyuk GA, Grot A, O'Leary SE, Puglisi JD, Williamson JR. Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts. Nature Communications. 9: 5087. PMID 30504830 DOI: 10.1038/s41467-018-07423-3  0.96
2018 Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nature Methods. 15: 947-954. PMID 30377372 DOI: 10.1038/s41592-018-0172-2  0.4
2018 Coey AT, Larsen KP, Choi J, Barrero DJ, Puglisi JD, Puglisi EV. Dynamic Interplay of RNA and Protein in the Human Immunodeficiency Virus-1 Reverse Transcription Initiation Complex. Journal of Molecular Biology. PMID 30201267 DOI: 10.1016/j.jmb.2018.08.029  0.4
2018 Choi J, Grosely R, Prabhakar A, Lapointe CP, Wang J, Puglisi JD. How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation. Annual Review of Biochemistry. 87: 421-449. PMID 29925264 DOI: 10.1146/annurev-biochem-060815-014818  0.4
2018 Prabhakar A, Puglisi EV, Puglisi JD. Single-Molecule Fluorescence Applied to Translation. Cold Spring Harbor Perspectives in Biology. PMID 29891562 DOI: 10.1101/cshperspect.a032714  0.4
2018 Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV. Architecture of an HIV-1 reverse transcriptase initiation complex. Nature. PMID 29695867 DOI: 10.1038/s41586-018-0055-9  0.4
2018 Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD. 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation. Nature Structural & Molecular Biology. PMID 29459784 DOI: 10.1038/s41594-018-0030-z  0.88
2017 Choi J, Puglisi JD. Three tRNAs on the ribosome slow translation elongation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29229848 DOI: 10.1073/pnas.1719592115  0.4
2017 Johnson AG, Petrov AN, Fuchs G, Majzoub K, Grosely R, Choi J, Puglisi JD. Fluorescently-tagged human eIF3 for single-molecule spectroscopy. Nucleic Acids Research. PMID 29136179 DOI: 10.1093/nar/gkx1050  0.4
2017 Prabhakar A, Capece MC, Petrov A, Choi J, Puglisi JD. Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling. Cell Reports. 20: 161-172. PMID 28683310 DOI: 10.1016/j.celrep.2017.06.028  0.88
2017 Prabhakar A, Choi J, Wang J, Petrov A, Puglisi JD. Dynamic basis of fidelity and speed in translation: Coordinated multi-step mechanisms of elongation and termination. Protein Science : a Publication of the Protein Society. PMID 28480640 DOI: 10.1002/pro.3190  0.88
2017 Johnson AG, Grosely R, Petrov AN, Puglisi JD. Dynamics of IRES-mediated translation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 372. PMID 28138065 DOI: 10.1098/rstb.2016.0177  0.4
2016 Chen J, Choi J, O'Leary SE, Prabhakar A, Petrov A, Grosely R, Puglisi EV, Puglisi JD. The molecular choreography of protein synthesis: translational control, regulation, and pathways. Quarterly Reviews of Biophysics. 49: e11. PMID 27658712 DOI: 10.1017/S0033583516000056  0.88
2016 Coey A, Larsen K, Puglisi JD, Puglisi EV. Heterogeneous structures formed by conserved RNA sequences within the HIV reverse transcription initiation site. Rna (New York, N.Y.). PMID 27613581 DOI: 10.1261/rna.056804.116  0.4
2016 Navon SP, Kornberg G, Chen J, Schwartzman T, Tsai A, Puglisi EV, Puglisi JD, Adir N. Amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences. Proceedings of the National Academy of Sciences of the United States of America. PMID 27307442 DOI: 10.1073/pnas.1606518113  0.4
2016 Petrov A, Grosely R, Chen J, O'Leary SE, Puglisi JD. Multiple Parallel Pathways of Translation Initiation on the CrPV IRES. Molecular Cell. 62: 92-103. PMID 27058789 DOI: 10.1016/j.molcel.2016.03.020  1
2016 Tsai A, Puglisi JD, Uemura S. Probing the Translation Dynamics of Ribosomes Using Zero-Mode Waveguides. Progress in Molecular Biology and Translational Science. 139: 1-43. PMID 26970189 DOI: 10.1016/bs.pmbts.2015.10.006  1
2016 Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD. N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nature Structural & Molecular Biology. PMID 26751643 DOI: 10.1038/nsmb.3148  1
2015 Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, ... ... Puglisi JD, et al. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nature Methods. PMID 26619013 DOI: 10.1038/nmeth.3667  0.4
2015 Chen J, Coakley A, O'Connor M, Petrov A, O'Leary SE, Atkins JF, Puglisi JD. Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions. Cell. 163: 1267-80. PMID 26590426 DOI: 10.1016/j.cell.2015.10.064  1
2015 Nilsson OB, Hedman R, Marino J, Wickles S, Bischoff L, Johansson M, Müller-Lucks A, Trovato F, Puglisi JD, O'Brien EP, Beckmann R, von Heijne G. Cotranslational Protein Folding inside the Ribosome Exit Tunnel. Cell Reports. 12: 1533-40. PMID 26321634 DOI: 10.1016/j.celrep.2015.07.065  1
2015 Puglisi JD. Synthetic biology: Ribosomal ties that bind. Nature. 524: 45-6. PMID 26222027 DOI: 10.1038/nature14642  1
2015 Puglisi JD. Protein synthesis. The delicate dance of translation and folding. Science (New York, N.Y.). 348: 399-400. PMID 25908811 DOI: 10.1126/science.aab2157  1
2015 Puglisi JD. RNA dances to center stage. Rna (New York, N.Y.). 21: 712-3. PMID 25780204 DOI: 10.1261/rna.051078.115  1
2015 Capece MC, Kornberg GL, Petrov A, Puglisi JD. A simple real-time assay for in vitro translation. Rna (New York, N.Y.). 21: 296-305. PMID 25525154 DOI: 10.1261/rna.047159.114  1
2015 Fuchs G, Petrov AN, Marceau CD, Popov LM, Chen J, O'Leary SE, Wang R, Carette JE, Sarnow P, Puglisi JD. Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site. Proceedings of the National Academy of Sciences of the United States of America. 112: 319-25. PMID 25516984 DOI: 10.1073/pnas.1421328111  1
2014 Noriega TR, Chen J, Walter P, Puglisi JD. Real-time observation of signal recognition particle binding to actively translating ribosomes. Elife. 3. PMID 25358118 DOI: 10.7554/eLife.04418  0.4
2014 Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD. Dynamic pathways of -1 translational frameshifting. Nature. 512: 328-32. PMID 24919156 DOI: 10.1038/nature13428  1
2014 Tsai A, Kornberg G, Johansson M, Chen J, Puglisi JD. The dynamics of SecM-induced translational stalling. Cell Reports. 7: 1521-33. PMID 24836001 DOI: 10.1016/j.celrep.2014.04.033  1
2014 Johansson M, Chen J, Tsai A, Kornberg G, Puglisi JD. Sequence-dependent elongation dynamics on macrolide-bound ribosomes. Cell Reports. 7: 1534-46. PMID 24836000 DOI: 10.1016/j.celrep.2014.04.034  1
2014 Noriega TR, Tsai A, Elvekrog MM, Petrov A, Neher SB, Chen J, Bradshaw N, Puglisi JD, Walter P. Signal recognition particle-ribosome binding is sensitive to nascent chain length. The Journal of Biological Chemistry. 289: 19294-305. PMID 24808175 DOI: 10.1074/jbc.M114.563239  1
2014 Chen J, Dalal RV, Petrov AN, Tsai A, O'Leary SE, Chapin K, Cheng J, Ewan M, Hsiung PL, Lundquist P, Turner SW, Hsu DR, Puglisi JD. High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence. Proceedings of the National Academy of Sciences of the United States of America. 111: 664-9. PMID 24379388 DOI: 10.1073/pnas.1315735111  1
2013 O'Leary SE, Petrov A, Chen J, Puglisi JD. Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure (London, England : 1993). 21: 2197-207. PMID 24183571 DOI: 10.1016/j.str.2013.09.016  1
2013 Petrov A, Wu T, Puglisi EV, Puglisi JD. RNA purification by preparative polyacrylamide gel electrophoresis. Methods in Enzymology. 530: 315-30. PMID 24034329 DOI: 10.1016/B978-0-12-420037-1.00017-8  1
2013 Petrov A, Tsa A, Puglisi JD. Analysis of RNA by analytical polyacrylamide gel electrophoresis. Methods in Enzymology. 530: 301-13. PMID 24034328 DOI: 10.1016/B978-0-12-420037-1.00016-6  1
2013 Simonetti A, Marzi S, Billas IM, Tsai A, Fabbretti A, Myasnikov AG, Roblin P, Vaiana AC, Hazemann I, Eiler D, Steitz TA, Puglisi JD, Gualerzi CO, Klaholz BP. Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. Proceedings of the National Academy of Sciences of the United States of America. 110: 15656-61. PMID 24029017 DOI: 10.1073/pnas.1309578110  1
2013 Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD. Coordinated conformational and compositional dynamics drive ribosome translocation. Nature Structural & Molecular Biology. 20: 718-27. PMID 23624862 DOI: 10.1038/nsmb.2567  1
2013 Tsai A, Uemura S, Johansson M, Puglisi EV, Marshall RA, Aitken CE, Korlach J, Ehrenberg M, Puglisi JD. The impact of aminoglycosides on the dynamics of translation elongation. Cell Reports. 3: 497-508. PMID 23416053 DOI: 10.1016/j.celrep.2013.01.027  1
2013 Puglisi EV, Puglisi JD. Using NMR to determine the conformation of the HIV reverse transcription initiation complex Nato Science For Peace and Security Series B: Physics and Biophysics. 97-119. DOI: 10.1007/978-94-007-4923-8-7  1
2012 Chen J, Tsai A, O'Leary SE, Petrov A, Puglisi JD. Unraveling the dynamics of ribosome translocation. Current Opinion in Structural Biology. 22: 804-14. PMID 23142574 DOI: 10.1016/j.sbi.2012.09.004  1
2012 Petrov A, Chen J, O'Leary S, Tsai A, Puglisi JD. Single-molecule analysis of translational dynamics. Cold Spring Harbor Perspectives in Biology. 4: a011551. PMID 22798542 DOI: 10.1101/cshperspect.a011551  1
2012 Harvey CJ, Puglisi JD, Pande VS, Cane DE, Khosla C. Precursor directed biosynthesis of an orthogonally functional erythromycin analogue: selectivity in the ribosome macrolide binding pocket. Journal of the American Chemical Society. 134: 12259-65. PMID 22741553 DOI: 10.1021/ja304682q  1
2012 Tsai A, Petrov A, Marshall RA, Korlach J, Uemura S, Puglisi JD. Heterogeneous pathways and timing of factor departure during translation initiation. Nature. 487: 390-3. PMID 22722848 DOI: 10.1038/nature11172  1
2012 Puglisi JD, Williamson JR. Digging deep into nucleic acid structure and nucleic acid protein recognition. Current Opinion in Structural Biology. 22: 249-50. PMID 22632873 DOI: 10.1016/j.sbi.2012.05.003  1
2012 Chen J, Tsai A, Petrov A, Puglisi JD. Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics. Journal of the American Chemical Society. 134: 5734-7. PMID 22428667 DOI: 10.1021/ja2119964  1
2012 Masuda T, Petrov AN, Iizuka R, Funatsu T, Puglisi JD, Uemura S. Initiation factor 2, tRNA, and 50S subunits cooperatively stabilize mRNAs on the ribosome during initiation. Proceedings of the National Academy of Sciences of the United States of America. 109: 4881-5. PMID 22411833 DOI: 10.1073/pnas.1118452109  1
2011 Puglisi EV, Puglisi JD. Secondary structure of the HIV reverse transcription initiation complex by NMR. Journal of Molecular Biology. 410: 863-74. PMID 21763492 DOI: 10.1016/j.jmb.2011.04.024  1
2011 Petrov A, Kornberg G, O'Leary S, Tsai A, Uemura S, Puglisi JD. Dynamics of the translational machinery. Current Opinion in Structural Biology. 21: 137-45. PMID 21256733 DOI: 10.1016/j.sbi.2010.11.007  1
2010 Aitken CE, Puglisi JD. Following the intersubunit conformation of the ribosome during translation in real time. Nature Structural & Molecular Biology. 17: 793-800. PMID 20562856 DOI: 10.1038/nsmb.1828  1
2010 Puglisi JD, Williamson JR. Nucleic acids continue to surprise. Current Opinion in Structural Biology. 20: 259-61. PMID 20510604 DOI: 10.1016/j.sbi.2010.04.005  1
2010 Petrov A, Puglisi JD. Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations. Nucleic Acids Research. 38: e143. PMID 20501598 DOI: 10.1093/nar/gkq390  1
2010 Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, Puglisi JD. Real-time tRNA transit on single translating ribosomes at codon resolution. Nature. 464: 1012-7. PMID 20393556 DOI: 10.1038/nature08925  1
2010 Aitken CE, Petrov A, Puglisi JD. Single ribosome dynamics and the mechanism of translation. Annual Review of Biophysics. 39: 491-513. PMID 20192783 DOI: 10.1146/annurev.biophys.093008.131427  1
2010 Bokoch MP, Zou Y, Rasmussen SG, Liu CW, Nygaard R, Rosenbaum DM, Fung JJ, Choi HJ, Thian FS, Kobilka TS, Puglisi JD, Weis WI, Pardo L, Prosser RS, Mueller L, et al. Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor. Nature. 463: 108-12. PMID 20054398 DOI: 10.1038/nature08650  1
2009 Puglisi JD. Resolving the elegant architecture of the ribosome. Molecular Cell. 36: 720-3. PMID 20005832 DOI: 10.1016/j.molcel.2009.11.031  1
2009 Elazar M, Liu M, McKenna SA, Liu P, Gehrig EA, Puglisi JD, Rossignol JF, Glenn JS. The anti-hepatitis C agent nitazoxanide induces phosphorylation of eukaryotic initiation factor 2alpha via protein kinase activated by double-stranded RNA activation. Gastroenterology. 137: 1827-35. PMID 19664635 DOI: 10.1053/j.gastro.2009.07.056  1
2009 Marshall RA, Aitken CE, Puglisi JD. GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Molecular Cell. 35: 37-47. PMID 19595714 DOI: 10.1016/j.molcel.2009.06.008  1
2009 Shimoike T, McKenna SA, Lindhout DA, Puglisi JD. Translational insensitivity to potent activation of PKR by HCV IRES RNA. Antiviral Research. 83: 228-37. PMID 19467267 DOI: 10.1016/j.antiviral.2009.05.004  1
2009 Liu CW, Alekseyev VY, Allwardt JR, Bankovich AJ, Cade-Menun BJ, Davis RW, Du LS, Garcia KC, Herschlag D, Khosla C, Kraut DA, Li Q, Null B, Puglisi JD, Sigala PA, et al. The diversity of nuclear magnetic resonance spectroscopy Nato Science For Peace and Security Series B: Physics and Biophysics. 65-81.  1
2008 Marshall RA, Dorywalska M, Puglisi JD. Irreversible chemical steps control intersubunit dynamics during translation. Proceedings of the National Academy of Sciences of the United States of America. 105: 15364-9. PMID 18824686 DOI: 10.1073/pnas.0805299105  1
2008 Marshall RA, Aitken CE, Dorywalska M, Puglisi JD. Translation at the single-molecule level. Annual Review of Biochemistry. 77: 177-203. PMID 18518820 DOI: 10.1146/annurev.biochem.77.070606.101431  1
2008 Uemura S, Iizuka R, Ueno T, Shimizu Y, Taguchi H, Ueda T, Puglisi JD, Funatsu T. Single-molecule imaging of full protein synthesis by immobilized ribosomes. Nucleic Acids Research. 36: e70. PMID 18511463 DOI: 10.1093/nar/gkn338  1
2008 Aitken CE, Marshall RA, Puglisi JD. An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophysical Journal. 94: 1826-35. PMID 17921203 DOI: 10.1529/biophysj.107.117689  1
2007 Puglisi JD. Structural biology: the dance of domains. Nature. 450: 1171-2. PMID 18097392 DOI: 10.1038/4501171a  1
2007 McKenna SA, Kim I, Puglisi EV, Lindhout DA, Aitken CE, Marshall RA, Puglisi JD. Purification and characterization of transcribed RNAs using gel filtration chromatography. Nature Protocols. 2: 3270-7. PMID 18079727 DOI: 10.1038/nprot.2007.480  1
2007 Puglisi EV, Puglisi JD. Probing the conformation of human tRNA(3)(Lys) in solution by NMR. Febs Letters. 581: 5307-14. PMID 17963705 DOI: 10.1016/j.febslet.2007.10.026  1
2007 Gonzalez RL, Chu S, Puglisi JD. Thiostrepton inhibition of tRNA delivery to the ribosome. Rna (New York, N.Y.). 13: 2091-7. PMID 17951333 DOI: 10.1261/rna.499407  1
2007 McKenna SA, Lindhout DA, Shimoike T, Puglisi JD. Biophysical and biochemical investigations of dsRNA-activated kinase PKR. Methods in Enzymology. 430: 373-96. PMID 17913645 DOI: 10.1016/S0076-6879(07)30014-1  0.36
2007 Alekseyev VY, Liu CW, Cane DE, Puglisi JD, Khosla C. Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Protein Science : a Publication of the Protein Society. 16: 2093-107. PMID 17893358 DOI: 10.1110/ps.073011407  1
2007 Lee TH, Blanchard SC, Kim HD, Puglisi JD, Chu S. The role of fluctuations in tRNA selection by the ribosome. Proceedings of the National Academy of Sciences of the United States of America. 104: 13661-5. PMID 17699629 DOI: 10.1073/pnas.0705988104  1
2007 Kim HD, Puglisi JD, Chu S. Fluctuations of transfer RNAs between classical and hybrid states. Biophysical Journal. 93: 3575-82. PMID 17693476 DOI: 10.1529/biophysj.107.109884  1
2007 Varani L, Bankovich AJ, Liu CW, Colf LA, Jones LL, Kranz DM, Puglisi JD, Garcia KC. Solution mapping of T cell receptor docking footprints on peptide-MHC. Proceedings of the National Academy of Sciences of the United States of America. 104: 13080-5. PMID 17670943 DOI: 10.1073/pnas.0703702104  1
2007 McKenna SA, Lindhout DA, Shimoike T, Aitken CE, Puglisi JD. Viral dsRNA inhibitors prevent self-association and autophosphorylation of PKR. Journal of Molecular Biology. 372: 103-13. PMID 17619024 DOI: 10.1016/j.jmb.2007.06.028  1
2007 Uemura S, Dorywalska M, Lee TH, Kim HD, Puglisi JD, Chu S. Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. Nature. 446: 454-7. PMID 17377584 DOI: 10.1038/nature05625  1
2007 McKenna SA, Lindhout DA, Kim I, Liu CW, Gelev VM, Wagner G, Puglisi JD. Molecular framework for the activation of RNA-dependent protein kinase. The Journal of Biological Chemistry. 282: 11474-86. PMID 17284445 DOI: 10.1074/jbc.M700301200  1
2007 Kim I, McKenna SA, Viani Puglisi E, Puglisi JD. Rapid purification of RNAs using fast performance liquid chromatography (FPLC). Rna (New York, N.Y.). 13: 289-94. PMID 17179067 DOI: 10.1261/rna.342607  1
2007 Lindhout DA, McKenna SA, Echeverría Aitken C, Liu CW, Puglisi JD. PKR: A NMR perspective Progress in Nuclear Magnetic Resonance Spectroscopy. 51: 199-215. DOI: 10.1016/j.pnmrs.2007.07.001  1
2007 Marshall RA, Puglisi JD. NMR Structural Studies of Aminoglycoside: RNA Interaction Aminoglycoside Antibiotics: From Chemical Biology to Drug Discovery. 181-207. DOI: 10.1002/9780470149676.ch5  1
2006 McKenna SA, Kim I, Liu CW, Puglisi JD. Uncoupling of RNA binding and PKR kinase activation by viral inhibitor RNAs. Journal of Molecular Biology. 358: 1270-85. PMID 16580685 DOI: 10.1016/j.jmb.2006.03.003  1
2006 Kim I, Liu CW, Puglisi JD. Specific recognition of HIV TAR RNA by the dsRNA binding domains (dsRBD1-dsRBD2) of PKR. Journal of Molecular Biology. 358: 430-42. PMID 16516925 DOI: 10.1016/j.jmb.2006.01.099  1
2006 Lima C, Puglisi JD, Sali A, Szewczak L. Editorial Structure. 14: 801. DOI: 10.1016/j.str.2006.05.005  1
2005 Underwood KA, Swartz JR, Puglisi JD. Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis. Biotechnology and Bioengineering. 91: 425-35. PMID 15991235 DOI: 10.1002/bit.20529  1
2005 Lukavsky PJ, Puglisi JD. Structure determination of large biological RNAs. Methods in Enzymology. 394: 399-416. PMID 15808230 DOI: 10.1016/S0076-6879(05)94016-0  1
2005 Dorywalska M, Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD. Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Research. 33: 182-9. PMID 15647501 DOI: 10.1093/nar/gki151  1
2004 Otto GA, Puglisi JD. The pathway of HCV IRES-mediated translation initiation. Cell. 119: 369-80. PMID 15507208 DOI: 10.1016/j.cell.2004.09.038  1
2004 Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD. tRNA selection and kinetic proofreading in translation. Nature Structural & Molecular Biology. 11: 1008-14. PMID 15448679 DOI: 10.1038/nsmb831  1
2004 Blanchard SC, Kim HD, Gonzalez RL, Puglisi JD, Chu S. tRNA dynamics on the ribosome during translation. Proceedings of the National Academy of Sciences of the United States of America. 101: 12893-8. PMID 15317937 DOI: 10.1073/pnas.0403884101  1
2004 Lukavsky PJ, Puglisi JD. Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. Rna (New York, N.Y.). 10: 889-93. PMID 15100443 DOI: 10.1261/rna.5264804  1
2003 Runyon ST, Puglisi JD. Design of a cyclic peptide that targets a viral RNA. Journal of the American Chemical Society. 125: 15704-5. PMID 14677935 DOI: 10.1021/ja036344h  1
2003 Schroeder SJ, Fountain MA, Kennedy SD, Lukavsky PJ, Puglisi JD, Krugh TR, Turner DH. Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron. Biochemistry. 42: 14184-96. PMID 14640686 DOI: 10.1021/bi0301587  1
2003 Lukavsky PJ, Kim I, Otto GA, Puglisi JD. Structure of HCV IRES domain II determined by NMR. Nature Structural Biology. 10: 1033-8. PMID 14578934 DOI: 10.1038/nsb1004  1
2003 Li Q, Khosla C, Puglisi JD, Liu CW. Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein. Biochemistry. 42: 4648-57. PMID 12705828 DOI: 10.1021/bi0274120  1
2003 Lynch SR, Gonzalez RL, Puglisi JD. Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Structure (London, England : 1993). 11: 43-53. PMID 12517339 DOI: 10.1016/S0969-2126(02)00934-6  1
2002 Kim I, Lukavsky PJ, Puglisi JD. NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling. Journal of the American Chemical Society. 124: 9338-9. PMID 12167005 DOI: 10.1021/ja026647w  1
2002 Otto GA, Lukavsky PJ, Lancaster AM, Sarnow P, Puglisi JD. Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction. Rna (New York, N.Y.). 8: 913-23. PMID 12166646 DOI: 10.1017/S1355838202022057  1
2002 Yoshizawa S, Fourmy D, Eason RG, Puglisi JD. Sequence-specific recognition of the major groove of RNA by deoxystreptamine. Biochemistry. 41: 6263-70. PMID 12009887 DOI: 10.1021/bi0121609  1
2001 Puglisi JD, Kim I, Lukavsky P, Otto G, Lancaster A, Sarnow P. Structural and functional investigation of the hepatitis C virus IRES. Nucleic Acids Research. Supplement (2001). 263. PMID 12836365  1
2001 Lukavsky PJ, Puglisi JD. RNAPack: an integrated NMR approach to RNA structure determination. Methods (San Diego, Calif.). 25: 316-32. PMID 11860286 DOI: 10.1006/meth.2001.1244  1
2001 Recht MI, Puglisi JD. Aminoglycoside resistance with homogeneous and heterogeneous populations of antibiotic-resistant ribosomes. Antimicrobial Agents and Chemotherapy. 45: 2414-9. PMID 11502507 DOI: 10.1128/AAC.45.9.2414-2419.2001  1
2001 Blanchard SC, Puglisi JD. Solution structure of the A loop of 23S ribosomal RNA. Proceedings of the National Academy of Sciences of the United States of America. 98: 3720-5. PMID 11259644 DOI: 10.1073/pnas.051608498  1
2001 Lynch SR, Puglisi JD. Structural origins of aminoglycoside specificity for prokaryotic ribosomes. Journal of Molecular Biology. 306: 1037-58. PMID 11237617 DOI: 10.1006/jmbi.2000.4420  1
2001 Lynch SR, Puglisi JD. Structure of a eukaryotic decoding region A-site RNA. Journal of Molecular Biology. 306: 1023-35. PMID 11237616 DOI: 10.1006/jmbi.2000.4419  1
2000 Lukavsky PJ, Otto GA, Lancaster AM, Sarnow P, Puglisi JD. Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. Nature Structural Biology. 7: 1105-10. PMID 11101890 DOI: 10.1038/81951  1
2000 Puglisi JD, Blanchard SC, Green R. Approaching translation at atomic resolution. Nature Structural Biology. 7: 855-61. PMID 11017192 DOI: 10.1038/79603  1
2000 Dahlquist KD, Puglisi JD. Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. Journal of Molecular Biology. 299: 1-15. PMID 10860719 DOI: 10.1006/jmbi.2000.3672  1
2000 Lynch SR, Recht MI, Puglisi JD. Biochemical and nuclear magnetic resonance studies of aminoglycoside-RNA complexes. Methods in Enzymology. 317: 240-61. PMID 10829284  1
2000 Puglisi JD. mRNA processing: the 3'-end justifies the means. Nature Structural Biology. 7: 263-4. PMID 10742163 DOI: 10.1038/74008  1
2000 Lynch SR, Puglisi JD. Application of residual dipolar coupling measurements to identify conformational changes in RNA induced by antibiotics [22] Journal of the American Chemical Society. 122: 7853-7854. DOI: 10.1021/ja000284n  1
1999 Green R, Puglisi JD. The ribosome revealed. Nature Structural Biology. 6: 999-1003. PMID 10542087 DOI: 10.1038/14881  1
1999 Yoshizawa S, Fourmy D, Puglisi JD. Recognition of the codon-anticodon helix by ribosomal RNA. Science (New York, N.Y.). 285: 1722-5. PMID 10481006 DOI: 10.1126/science.285.5434.1722  1
1999 Recht MI, Douthwaite S, Puglisi JD. Basis for prokaryotic specificity of action of aminoglycoside antibiotics. The Embo Journal. 18: 3133-8. PMID 10357824 DOI: 10.1093/emboj/18.11.3133  1
1999 Recht MI, Douthwaite S, Dahlquist KD, Puglisi JD. Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction. Journal of Molecular Biology. 286: 33-43. PMID 9931247 DOI: 10.1006/jmbi.1998.2446  1
1998 Puglisi EV, Puglisi JD. HIV-1 A-rich RNA loop mimics the tRNA anticodon structure. Nature Structural Biology. 5: 1033-6. PMID 9846871 DOI: 10.1038/4141  1
1998 Yoshizawa S, Fourmy D, Puglisi JD. Structural origins of gentamicin antibiotic action. The Embo Journal. 17: 6437-48. PMID 9822590 DOI: 10.1093/emboj/17.22.6437  1
1998 Blanchard SC, Fourmy D, Eason RG, Puglisi JD. rRNA chemical groups required for aminoglycoside binding. Biochemistry. 37: 7716-24. PMID 9601031 DOI: 10.1021/bi973125y  1
1998 Fourmy D, Recht MI, Puglisi JD. Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA. Journal of Molecular Biology. 277: 347-62. PMID 9514735 DOI: 10.1006/jmbi.1997.1552  1
1998 Fourmy D, Yoshizawa S, Puglisi JD. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. Journal of Molecular Biology. 277: 333-45. PMID 9514734 DOI: 10.1006/jmbi.1997.1551  1
1997 Puglisi EV, Green R, Noller HF, Puglisi JD. Structure of a conserved RNA component of the peptidyl transferase centre. Nature Structural Biology. 4: 775-8. PMID 9334738  1
1996 Fourmy D, Recht MI, Blanchard SC, Puglisi JD. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science (New York, N.Y.). 274: 1367-71. PMID 8910275 DOI: 10.1126/science.274.5291.1367  1
1996 Recht MI, Fourmy D, Blanchard SC, Dahlquist KD, Puglisi JD. RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. Journal of Molecular Biology. 262: 421-36. PMID 8893854 DOI: 10.1006/jmbi.1996.0526  1
1995 Puglisi JD, Chen L, Blanchard S, Frankel AD. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex Science. 270: 1200-1203. PMID 7502045 DOI: 10.1126/science.270.5239.1200  1
1994 Puglisi EV, Puglisi JD, Williamson JR, RajBhandary UL. NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end. Proceedings of the National Academy of Sciences of the United States of America. 91: 11467-71. PMID 7972085 DOI: 10.1073/pnas.91.24.11467  1
1993 Puglisi JD, Pütz J, Florentz C, Giegé R. Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase. Nucleic Acids Research. 21: 41-9. PMID 8441619  0.76
1993 Giegé R, Puglisi JD, Florentz C. tRNA structure and aminoacylation efficiency. Progress in Nucleic Acid Research and Molecular Biology. 45: 129-206. PMID 8341800 DOI: 10.1016/S0079-6603(08)60869-7  1
1993 Pütz J, Puglisi JD, Florentz C, Giegé R. Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA. The Embo Journal. 12: 2949-57. PMID 8335008  0.76
1993 Puglisi JD, Chen L, Frankel AD, Williamson JR. Role of RNA structure in arginine recognition of TAR RNA. Proceedings of the National Academy of Sciences of the United States of America. 90: 3680-4. PMID 7682716 DOI: 10.1073/pnas.90.8.3680  0.96
1992 Perret V, Florentz C, Puglisi JD, Giegé R. Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities. Journal of Molecular Biology. 226: 323-33. PMID 1640453 DOI: 10.1016/0022-2836(92)90950-O  1
1992 Rudinger J, Puglisi JD, Pütz J, Schatz D, Eckstein F, Florentz C, Giegé R. Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase. Proceedings of the National Academy of Sciences of the United States of America. 89: 5882-6. PMID 1631068  1
1992 Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science (New York, N.Y.). 257: 76-80. PMID 1621097 DOI: 10.1126/science.1621097  0.96
1992 Batey RT, Inada M, Kujawinski E, Puglisi JD, Williamson JR. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucleic Acids Research. 20: 4515-23. PMID 1383928  1
1991 Pütz J, Puglisi JD, Florentz C, Giegé R. Identity elements for specific aminoacylation of yeast tRNA(Asp) by cognate aspartyl-tRNA synthetase. Science (New York, N.Y.). 252: 1696-9. PMID 2047878  0.76
1990 Giegé R, Florentz C, Garcia A, Grosjean H, Perret V, Puglisi J, Théobald-Dietrich A, Ebel JP. Exploring the aminoacylation function of transfer RNA by macromolecular engineering approaches. Involvement of conformational features in the charging process of yeast tRNA(Asp). Biochimie. 72: 453-61. PMID 2124148  0.76
1990 Perret V, Garcia A, Puglisi J, Grosjean H, Ebel JP, Florentz C, Giegé R. Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. Biochimie. 72: 735-43. PMID 2078590  0.76
1990 Wyatt JR, Puglisi JD, Tinoco I. RNA pseudoknots. Stability and loop size requirements. Journal of Molecular Biology. 214: 455-70. PMID 1696319 DOI: 10.1016/0022-2836(90)90193-P  1
1990 Puglisi JD, Wyatt JR, Tinoco I. Conformation of an RNA pseudoknot. Journal of Molecular Biology. 214: 437-53. PMID 1696318 DOI: 10.1016/0022-2836(90)90192-O  1
1990 Puglisi JD, Wyatt JR, Tinoco I. Solution conformation of an RNA hairpin loop. Biochemistry. 29: 4215-26. PMID 1694459  1
1989 Wyatt JR, Puglisi JD, Tinoco I. RNA folding: pseudoknots, loops and bulges. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 11: 100-6. PMID 2695075 DOI: 10.1002/bies.950110406  1
1989 Puglisi JD, Tinoco I. Absorbance melting curves of RNA. Methods in Enzymology. 180: 304-25. PMID 2482421  1
1988 Puglisi JD, Wyatt JR, Tinoco I. A pseudoknotted RNA oligonucleotide. Nature. 331: 283-6. PMID 3336440 DOI: 10.1038/331283a0  1
1987 Tinoco I, Davis PW, Hardin CC, Puglisi JD, Walker GT, Wyatt J. RNA structure from A to Z. Cold Spring Harbor Symposia On Quantitative Biology. 52: 135-46. PMID 2456875  1
1987 Trulson MO, Cruz P, Puglisi JD, Tinoco I, Mathies RA. Raman spectroscopic study of left-handed Z-RNA. Biochemistry. 26: 8624-30. PMID 2450564 DOI: 10.1021/bi00400a020  1
1987 Hardin CC, Zarling DA, Puglisi JD, Trulson MO, Davis PW, Tinoco I. Stabilization of Z-RNA by chemical bromination and its recognition by anti-Z-DNA antibodies. Biochemistry. 26: 5191-9. PMID 2444254  1
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