Puglisi
Lab
Our Publications

Publication Years
2018
Choi, J., Indrisiunaite, G., DeMirci, H., Ieong, K., Wang, J., Petrov, A., Prabhakar, A., Rechavi, G., Dominissini, D., He, C., Ehrenberg, M., Puglisi, J. D. How 2 '-O-Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation CELL PRESS. 2018: 592A
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Johnson, A. G., Puglisi, J. D. Single-Molecule Analysis of Ribosome and Factor Assembly Pathways on a Viral mRNA CELL PRESS. 2018: 595A
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Lapointe, C., Puglisi, J. Ribosomal Protein Dynamics on the Human Ribosome CELL PRESS. 2018: 595A
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Wang, J., Puglisi, J. D. Dynamics of Eukaryotic Translation Initiation CELL PRESS. 2018: 594A
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Larsen, K., Mathiharan, Y., Kappei, K., Coey, A., Chen, D., Madigan, L., Skiniotis, G., Puglisi, J., Puglisi, E. Structural Characterization of the HIV-1 Reverse Transcriptase Initiation Complex CELL PRESS. 2018: 193A
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Choi, J., Indrisiunaite, G., DeMirci, H., Ieong, K. W., Wang, J., Petrov, A., Prabhakar, A., Rechavi, G., Dominissini, D., He, C., Ehrenberg, M., Puglisi, J. D. 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation. Nature structural & molecular biology, 2018
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Larsen, K. P., Mathiharan, Y. K., Kappel, K., Coey, A. T., Chen, D. H., Barrero, D., Madigan, L., Puglisi, J. D., Skiniotis, G., Puglisi, E. V. Architecture of an HIV-1 reverse transcriptase initiation complex. Nature, 2018
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2017
Prabhakar, A., Choi, J., Wang, J., Petrov, A., Puglisi, J. D. Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination. Protein science, 2017
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Johnson, A. G., Grosely, R., Petrov, A. N., Puglisi, J. D. Dynamics of IRES-mediated translation PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2017; 372 (1716)
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Johnson, A. G., Petrov, A. N., Fuchs, G., Majzoub, K., Grosely, R., Choi, J., Puglisi, J. D. Fluorescently-tagged human eIF3 for single-molecule spectroscopy. Nucleic acids research 2017
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Choi, J., Puglisi, J. D. Three tRNAs on the ribosome slow translation elongation. Proceedings of the National Academy of Sciences of the United States of America, 2017; 114 (52): 13691–96
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Prabhakar A, Capece MC, Petrov A, Choi J, Puglisi JD. Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling. Cell Rep. 2017 Jul 5;20(1):161-172.
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Prabhakar A, Choi J, Wang J, Petrov A, Puglisi JD. Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination. Protein Sci. 2017 Jul;26(7):1352-1362.
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Johnson AG, Grosely R, Petrov AN, Puglisi JD. Dynamics of IRES-mediated translation. Philos Trans R Soc Lond B Biol Sci. 2017 Mar 19;372(1716).
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2016
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Navon, S. P., Kornberg, G., Chen, J., Schwartzman, T., Tsai, A., Puglisi, E. V., Puglisi, J. D., 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, 2016;
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Chen, J., Choi, J., O'Leary, S. E., Prabhakar, A., Petrov, A., Grosely, R., Puglisi, E. V., Puglisi, J. D. The molecular choreography of protein synthesis: translational control, regulation, and pathways QUARTERLY REVIEWS OF BIOPHYSICS, 2016; 49
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Petrov, A., Grosely, R., Chen, J., O'Leary, S. E., Puglisi, J. D. Multiple Parallel Pathways of Translation Initiation on the CrPV IRES. Molecular cell, 2016; 62 (1): 92-103
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Choi, J., Ieong, K., Demirci, H., Chen, J., Petrov, A., Prabhakar, A., O'Leary, S. E., Dominissini, D., Rechavi, G., Soltis, S. M., Ehrenberg, M., Puglisi, J. D. N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nature structural & molecular biology, 2016; 23 (2): 110-115
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Tsai, A., Puglisi, J. D., Uemura, S. Probing the Translation Dynamics of Ribosomes Using Zero-Mode Waveguides. Progress in molecular biology and translational science, 2016; 139: 1-43
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Siprashvili, Z., Webster, D. E., Johnston, D., Shenoy, R. M., Ungewickell, A. J., Bhaduri, A., Flockhart, R., Zarnegar, B. J., Che, Y., Meschi, F., Puglisi, J. D., Khavari, P. A. The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nature genetics, 2016; 48 (1): 53-58
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Sierra, R. G., Gati, C., Laksmono, H., Dao, E. H., Gul, S., Fuller, F., Kern, J., Chatterjee, R., Ibrahim, M., Brewster, A. S., Young, I. D., Michels-Clark, T., Aquila, A., Liang, M., Hunter, M. S., Koglin, J. E., Boutet, S., Junco, E. A., Hayes, B., Bogan, M. J., Hampton, C. Y., Puglisi, E. V., Sauter, N. K., Stan, C. A., Zouni, A., Yano, J., Yachandra, V. K., Soltis, S. M., Puglisi, J. D., DeMirci, H. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II NATURE METHODS,2016; 13 (1): 59-?
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2015
Chen, J., Coakley, A., O'Connor, M., Petrov, A., O'Leary, S. E., Atkins, J. F., Puglisi, J. D. Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions Cell, 2015; 163 (5): 1267-1280
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Nilsson, O. B., Hedman, R., Marino, J., Wickles, S., Bischoff, L., Johansson, M., Mueller-Lucks, A., Trovato, F., Puglisi, J. D., O'Brien, E. P., Beckmann, R., Von Heijne, G. Cotranslational Protein Folding inside the Ribosome Exit Tunnel Cell Reports, 2015; 12 (10): 1533-1540
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Puglisi, J. D. SYNTHETIC BIOLOGY Ribosomal ties that bind Nature, 2015; 524 (7563): 45-46
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Puglisi, J. D. Protein synthesis. The delicate dance of translation and folding. Science, 2015; 348 (6233): 399-400
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Puglisi, J. D. RNA dances to center stage RNA - A Publication of the RNA Society,2015; 21 (4): 712-713
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Capece, M. C., Kornberg, G. L., Petrov, A., Puglisi, J. D. A simple real-time assay for in vitro translation RNA, 2015; 21 (2): 296-305
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Fuchs, G., Petrov, A. N., Marceau, C. D., Popov, L. M., Chen, J., O'Leary, S. E., Wang, R., Carette, J. E., Sarnow, P., Puglisi, J. D. 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, 2015; 112 (2): 319-325
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2014
Noriega, T. R., Chen, J., Walter, P., Puglisi, J. D. Real-time observation of signal recognition particle binding to actively translating ribosomes eLife, 2014; 3
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Chen, J., Petrov, A., Johansson, M., Tsai, A., O'Leary, S. E., Puglisi, J. D. Dynamic pathways of -1 translational frameshifting. Nature, 2014; 512 (7514): 328-332
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Noriega, T. R., Tsai, A., Elvekrog, M. M., Petrov, A., Neher, S. B., Chen, J., Bradshaw, N., Puglisi, J. D., Walter, P. Signal Recognition Particle-ribosome Binding Is Sensitive to Nascent Chain Length Journal of Biological Chemistry, 2014; 289 (28): 19294-19305
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Tsai, A., Kornberg, G., Johansson, M., Chen, J., Puglisi, J. D. The Dynamics of SecM-Induced Translational Stalling Cell Reports, 2014; 7 (5): 1521-1533
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Johansson, M., Chen, J., Tsai, A., Kornberg, G., Puglisi, J. D. Sequence-Dependent Elongation Dynamics on Macrolide-Bound Ribosomes Cell Reports, 2014; 7 (5): 1534-1546
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Chen, J., Dalal, R. V., Petrov, A. N., Tsai, A., O'Leary, S. E., Chapin, K., Cheng, J., Ewan, M., Hsiung, P., Lundquist, P., Turner, S. W., Hsu, D. R., Puglisi, J. D. 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, 2014; 111 (2): 664-669
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2013
O'Leary, S. E., Petrov, A., Chen, J., Puglisi, J. D. Dynamic Recognition of the mRNA Cap by Saccharomyces cerevisiae eIF4E Structure, 2013; 21 (12): 2197-2207
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Simonetti, A., Marzi, S., Billas, I. M., Tsai, A., Fabbretti, A., Myasnikov, A. G., Roblin, P., Vaiana, A. C., Hazemann, I., Eiler, D., Steitz, T. A., Puglisi, J. D., Gualerzi, C. O., Klaholz, B. P. 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,2013; 110 (39): 15656-15661
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Chen, J., Petrov, A., Tsai, A., O'Leary, S. E., Puglisi, J. D. Coordinated conformational and compositional dynamics drive ribosome translocation. Nature structural & molecular biology, 2013; 20 (6): 718-727
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Tsai, A., Uemura, S., Johansson, M., Puglisi, E. V., Marshall, R. A., Aitken, C. E., Korlach, J., Ehrenberg, M., Puglisi, J. D. The Impact of Aminoglycosides on the Dynamics of Translation Elongation CELL REPORTS, 2013; 3 (2): 497-508
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Tsai, A., Chen, J., Kornberg, G., Korlach, J., Uemura, S., Puglisi, J. Observing Prokaryotic Translation Elongation in Real-Time using Single-Molecule Fluorescence CELL PRESS, 2013: 257A-257A
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Petrov, A., Tsa, A., Puglisi, J. D. Analysis of RNA by Analytical Polyacrylamide Gel Electrophoresis LABORATORY METHODS IN ENZYMOLOGY: RNA, 2013; 530: 301-313
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Petrov, A., Wu, T., Puglisi, E. V., Puglisi, J. D. RNA Purification by Preparative Polyacrylamide Gel Electrophoresis LABORATORY METHODS IN ENZYMOLOGY: RNA, 2013; 530: 315-330
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2012
Chen, J., Tsai, A., O'Leary, S. E., Petrov, A., Puglisi, J. D. Unraveling the dynamics of ribosome translocation CURRENT OPINION IN STRUCTURAL BIOLOGY,2012; 22 (6): 804-814
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Petrov, A., Chen, J., O'Leary, S., Tsai, A., Puglisi, J. D. Single-Molecule Analysis of Translational Dynamics COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY,2012; 4 (9)
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Harvey, C. J., Puglisi, J. D., Pande, V. S., Cane, D. E., Khosla, C. Precursor Directed Biosynthesis of an Orthogonally Functional Erythromycin Analogue: Selectivity in the Ribosome Macrolide Binding Pocket JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2012; 134 (29): 12259-12265
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Tsai, A., Petrov, A., Marshall, R. A., Korlach, J., Uemura, S., Puglisi, J. D. Heterogeneous pathways and timing of factor departure during translation initiation NATURE,2012; 487 (7407): 390-394
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Puglisi, J. D., Williamson, J. R. Digging deep into nucleic acid structure and nucleic acid protein recognition CURRENT OPINION IN STRUCTURAL BIOLOGY, 2012; 22 (3): 249-250
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Chen, J., Tsai, A., Petrov, A., Puglisi, J. D. Nonfluorescent Quenchers To Correlate Single-Molecule Conformational and Compositional Dynamics JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2012; 134 (13): 5734-5737
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Puglisi, J. D., Chen, J., Kornberg, G., O'Leary, S., Petrov, A., Tsai, A. Real-Time Dynamics of Translation FEDERATION AMER SOC EXP BIOL. 2012
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Masuda, T., Petrov, A. N., Iizuka, R., Funatsu, T., Puglisi, J. D., 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,2012; 109 (13): 4881-4885
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2011
Puglisi, E. V., Puglisi, J. D. Secondary Structure of the HIV Reverse Transcription Initiation Complex by NMR JOURNAL OF MOLECULAR BIOLOGY,2011; 410 (5): 863-874
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Petrov, A., Kornberg, G., O'Leary, S., Tsai, A., Uemura, S., Puglisi, J. D. Dynamics of the translational machinery CURRENT OPINION IN STRUCTURAL BIOLOGY, 2011; 21 (1): 137-145
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Uemura, S., Puglisi, J. D. Real-time monitoring of single-molecule translation RIBOSOMES: STRUCTURE, FUNCTION, AND DYNAMICS, 2011: 295-302
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2010
Petrov, A., Puglisi, J. D. Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations NUCLEIC ACIDS RESEARCH, 2010; 38 (13)
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Aitken, C. E., Puglisi, J. D. Following the intersubunit conformation of the ribosome during translation in real time NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2010; 17 (7): 793-U35
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Puglisi, J. D., Williamson, J. R. Nucleic acids continue to surprise Editorial overview CURRENT OPINION IN STRUCTURAL BIOLOGY, 2010; 20 (3): 259-261
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Uemura, S., Aitken, C. E., Korlach, J., Flusberg, B. A., Turner, S. W., Puglisi, J. D. Real-time tRNA transit on single translating ribosomes at codon resolution NATURE, 2010; 464 (7291): 1012-U73
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Bokoch, M. P., Zou, Y., Rasmussen, S. G., Liu, C. W., Nygaard, R., Rosenbaum, D. M., Fung, J. J., Choi, H., Thian, F. S., Kobilka, T. S., Puglisi, J. D., Weis, W. I., Pardo, L., Prosser, R. S., Mueller, L., Kobilka, B. K. Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor NATURE, 2010; 463 (7277): 108-U121
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Aitken, C. E., Petrov, A., Puglisi, J. D. Single Ribosome Dynamics and the Mechanism of Translation ANNUAL REVIEW OF BIOPHYSICS VOL 39, 2010; 39: 491-513
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2009
Puglisi, J. D. Resolving the Elegant Architecture of the Ribosome MOLECULAR CELL, 2009; 36 (5): 720-723
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Elazar, M., Liu, M., Mckenna, S. A., Liu, P., Gehrig, E. A., Puglisi, J. D., Rossignol, J., Glenn, J. S. The Anti-Hepatitis C Agent Nitazoxanide Induces Phosphorylation of Eukaryotic Initiation Factor 2 alpha Via Protein Kinase Activated by Double-Stranded RNA Activation GASTROENTEROLOGY, 2009; 137 (5): 1827-1835
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Shimoike, T., Mckenna, S. A., Lindhout, D. A., Puglisi, J. D. Translational insensitivity to potent activation of PKR by HCV IRES RNA ANTIVIRAL RESEARCH, 2009; 83 (3): 228-237
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Marshall, R. A., Aitken, C. E., Puglisi, J. D. GTP Hydrolysis by IF2 Guides Progression of the Ribosome into Elongation MOLECULAR CELL, 2009; 35 (1): 37-47
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Liu, C. W., Alekseyev, V. Y., Allwardt, J. R., Bankovich, A. J., Cade-Menun, B. J., Davis, R. W., Du, L., Garcia, K. C., Herschlag, D., Khosla, C., Kraut, D. A., Li, Q., Null, B., Puglisi, J. D., Sigala, P. A., Stebbins, J. F., Varani, L. THE DIVERSITY OF NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY NATO Advanced Study Institute on Biophysics and the Challenges of Emerging Threats, SPRINGER. 2009: 65–81
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Aitken, C. E., Marshall, R. A., Puglisi, J. D. Improved Dye Stability In Single-Molecule Fluorescence Experiments NATO Advanced Study Institute on Biophysics and the Challenges of Emerging Threats, SPRINGER. 2009: 83–99
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2008
Marshall, R. A., Dorywalska, M., Puglisi, J. D. Irreversible chemical steps control intersubunit dynamics during translation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008; 105 (40): 15364-15369
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Elazor, M., Liu, M., McKenna, S., Liu, P., Gehrig, E. A., Elfert, A., Puglisi, J., Rossignol, J., Glenn, J. S. Nitazoxanide (NTZ)is an Inducer EIF2A and PKR Phosphorylation 59th Annual Meeting of the American-Association-for-the-Study-of-Liver-Diseases, WILEY-BLACKWELL. 2008: 1151A–1151A
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Uemura, S., Iizuka, R., Ueno, T., Shimizu, Y., Taguchi, H., Ueda, T., Puglisi, J. D., Funatsu, T. Single-molecule imaging of full protein synthesis by immobilized ribosomes NUCLEIC ACIDS RESEARCH, 2008; 36 (12)
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Puglisi, J. D., Doudna, J. A. Nucleic acids and their protein partners CURRENT OPINION IN STRUCTURAL BIOLOGY, 2008; 18 (3): 279-281
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Aitken, C. E., Marshall, R. A., Puglisi, J. D. An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments BIOPHYSICAL JOURNAL, 2008; 94 (5): 1826-1835
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Marshall, R. A., Aitken, C. E., Dorywalska, M., Puglisi, J. D. Translation at the single-molecule level ANNUAL REVIEW OF BIOCHEMISTRY, 2008; 77: 177-203
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2007
Puglisi, J. D. Structural biology - The dance of domains NATURE, 2007; 450 (7173): 1171-1172
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Gonzalez, R. L., Chu, S., Puglisi, J. D. Thiostrepton inhibition of tRNA delivery to the ribosome RNA-A PUBLICATION OF THE RNA SOCIETY, 2007; 13 (12): 2091-2097
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Lindhout, D. A., Mckenna, S. A., Aitken, C. E., Liu, C. W., Puglisi, J. D. PKR: A NMR perspective PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 2007; 51 (3): 199-215
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Puglisi, E. V., Puglisi, J. D. Probing the conformation of human tRNA(3)(Lys) in solution by NMR FEBS LETTERS, 2007; 581 (27): 5307-5314
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Kim, H. D., Puglisi, J. D., Chu, S. Fluctuations of transfer RNAs between classical and hybrid states BIOPHYSICAL JOURNAL, 2007; 93 (10): 3575-3582
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Alekseyev, V. Y., Liu, C. W., Cane, D. E., Puglisi, J. D., Khosla, C. Solution structure and proposed domain-domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase PROTEIN SCIENCE, 2007; 16 (10): 2093-2107
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Mckenna, S. A., Lindhout, D. A., Shimoike, T., Aitken, C. E., Puglisi, J. D. Viral dsRNA inhibitors prevent self-association and autophosphorylation of PKR JOURNAL OF MOLECULAR BIOLOGY, 2007; 372 (1): 103-113
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Lee, T., Blanchard, S. C., Kim, H. D., Puglisi, J. D., 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, 2007; 104 (34): 13661-13665
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Varani, L., Bankovich, A. J., Liu, C. W., Colf, L. A., Jones, L. L., Kranz, D. M., Puglisi, J. D., Garcia, K. C. Solution mapping of T cell receptor docking footprints on peptide-MHC PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007; 104 (32): 13080-13085
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Mckenna, S. A., Lindhout, D. A., Kim, I., Liu, C. W., Gelev, V. M., Wagner, G., Puglisi, J. D. Molecular framework for the activation of RNA-dependent protein kinase JOURNAL OF BIOLOGICAL CHEMISTRY, 2007; 282 (15): 11474-11486
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Uemura, S., Dorywalska, M., Lee, T., Kim, H. D., Puglisi, J. D., Chu, S. Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome NATURE, 2007; 446 (7134): 454-457
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Kim, I., Mckenna, S. A., Puglisi, E. V., Puglisi, J. D. Rapid purification of RNAs using fast performance liquid chromatography (FPLC) RNA-A PUBLICATION OF THE RNA SOCIETY, 2007; 13 (2): 289-294
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Mckenna, S. A., Lindhout, D. A., Shimoike, T., Puglisi, J. D. Biophysical and biochemical investigations of dsRNA-activated kinase PKR TRANSLATION INITIATION: RECONSTITUTED SYSTEMS AND BIOPHYSICAL METHODS, 2007; 430: 373-396
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Uemura, S., Dorywalska, M., Lee, T., Kim, H. D., Puglisi, J. D., Chu, S. Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome 51st Annual Meeting of the Biophysical-Society, CELL PRESS. 2007: 571A–571A
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Mckenna, S. A., Lindhout, D. A., Aitken, C. E., Puglisi, J. D. Molecular insights into PKR activation by viral double-stranded RNA NATO Advanced Study Institute Course on Structure and Biophysics,SPRINGER. 2007: 99–110
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Mckenna, S. A., Kim, I., Puglisi, E. V., Lindhout, D. A., Aitken, C. E., Marshall, R. A., Puglisi, J. D. Purification and characterization of transcribed RNAs using gel filtration chromatography NATURE PROTOCOLS, 2007; 2 (12): 3270-3277
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Marshall RA, and Puglisi JD NMR structural studies of aminoglycoside:RNA interaction Aminoglycoside Antibiotics, Edited by DP Arya, John Wiley & Sons, 2007: 181-207
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McKenna SA, Lindhout DA, Aitken CE, Puglisi JD Molecular Insights Into PKR Activation by Viral Double-Stranded RNA NATO Science Series, Springer, 2007; Ch 8: 99-110
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2006
Lee, T., Blanchard, S. C., Kim, H. D., Puglisi, J. D., Chu, S. PHYS 336-Role of dynamics in the initial selection of tRNA by the ribosome AMERICAN CHEMICAL SOCIETY, 2006
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Kim, I., Liu, C. W., Puglisi, J. D. Specific recognition of HIV TAR RNA by the dsRNA binding domains (dsRBD1-dsRBD2) of PKR JOURNAL OF MOLECULAR BIOLOGY, 2006; 358 (2): 430-442
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2005
Underwood, K. A., Swartz, J. R., Puglisi, J. D. Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis BIOTECHNOLOGY AND BIOENGINEERING, 2005; 91 (4): 425-435
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Kim I, Lukavsky PJ, Otto GA, Liu CW, Puglisi JD Using NMR to Study large RNAs: Case Study of the HCV IRES NATO ASI Science Series, Ios Press, 2005; 364: 75-90
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Dorywalska, M., Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S., Puglisi, J. D. Site-specific labeling of the ribosome for single-molecule spectroscopy NUCLEIC ACIDS RESEARCH, 2005; 33 (1): 182-189
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Lukavsky, P. J., Puglisi, J. D. Structure determination of large biological RNAs NUCLEAR MAGNETIC RESONANCE OF BIOLOGICAL MACROMOLECULES, PART C, 2005; 394: 399-416
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2004
Otto, G. A., Puglisi, J. D. The pathway of HCVIRES-mediated translation initiation CELL, 2004; 119 (3): 369-380
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Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S., Puglisi, J. D. tRNA selection and kinetic proofreading in translation NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2004; 11 (10): 1008-1014
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Blanchard, S. C., Kim, H. D., Gonzalez, R. L., Puglisi, J. D., Chu, S. tRNA dynamics on the ribosome during translation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004; 101 (35): 12893-12898
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Lukavsky, P. J., Puglisi, J. D. Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides RNA-A PUBLICATION OF THE RNA SOCIETY, 2004; 10 (5): 889-893
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2003
Runyon, S. T., Puglisi, J. D. Design of a cyclic peptide that targets a viral RNA JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2003; 125 (51): 15704-15705
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Schroeder, S. J., Fountain, M. A., Kennedy, S. D., Lukavsky, P. J., Puglisi, J. D., Krugh, T. R., Turner, D. H. Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron BIOCHEMISTRY, 2003; 42 (48): 14184-14196
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Lukavsky, P. J., Kim, I., Otto, G. A., Puglisi, J. D. Structure of HCV IRES domain II determined by NMR NATURE STRUCTURAL BIOLOGY, 2003; 10 (12): 1033-1038
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Li, Q., Khosla, C., Puglisi, J. D., Liu, C. W. Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein BIOCHEMISTRY, 2003; 42 (16): 4648-4657
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2002
Kim, I., Lukavsky, P. J., Puglisi, J. D. NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2002; 124 (32): 9338-9339
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Otto, G. A., Lukavsky, P. J., Lancaster, A. M., Sarnow, P., Puglisi, J. D. Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction RNA-A PUBLICATION OF THE RNA SOCIETY, 2002; 8 (7): 913-923
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Yoshizawa, S., Fourmy, D., Eason, R. G., Puglisi, J. D. Sequence-specific recognition of the major groove of RNA by deoxystreptamine BIOCHEMISTRY, 2002; 41 (20): 6263-6270
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2001
Lukavsky, P. J., Puglisi, J. D. RNAPack: An integrated NMR approach to RNA structure determination METHODS, 2001; 25 (3): 316-332
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Recht, M. I., Puglisi, J. D. Aminoglycoside resistance with homogeneous and heterogeneous populations of antibiotic-resistant ribosomes ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2001; 45 (9): 2414-2419
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Blanchard, S. C., Puglisi, J. D. Solution structure of the A loop of 23S ribosomal RNA PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001; 98 (7): 3720-3725
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Lynch, S. R., Puglisi, J. D. Structural origins of aminoglycoside specificity for prokaryotic ribosomes JOURNAL OF MOLECULAR BIOLOGY, 2001; 306 (5): 1037-1058
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Lynch, S. R., Puglisi, J. D. Structure of a eukaryotic decoding region A-site RNA JOURNAL OF MOLECULAR BIOLOGY, 2001; 306 (5): 1023-1035
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Puglisi, J. D., 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), 2001: 263-?
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Puglisi, J. D., Yoshizawa, S., Fourmy, D. Molecular origins of ribosomal fidelity 4th NATO Advanced-Study-Institute on Dynamics, Structure and Function of Biological Macromolecules, I O S PRESS. 2001: 177–185
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2000
Lukavsky, P. J., Otto, G. A., Lancaster, A. M., Sarnow, P., Puglisi, J. D. Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function NATURE STRUCTURAL BIOLOGY, 2000; 7 (12): 1105-1110
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Puglisi, J. D., Blanchard, S. C., Green, R. Approaching translation at atomic resolution NATURE STRUCTURAL BIOLOGY, 2000; 7 (10): 855-861
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Lynch, S. R., Puglisi, J. D. Application of residual dipolar coupling measurements to identify conformational changes in RNA induced by antibiotics JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000; 122 (32): 7853-7854
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Dahlquist, K. D., Puglisi, J. D. Interaction of translation initiation factor IF1 with the E-coli ribosomal A site JOURNAL OF MOLECULAR BIOLOGY, 2000; 299 (1): 1-15
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Puglisi, J. D. mRNA processing: The 3 '-end justifies the means NATURE STRUCTURAL BIOLOGY, 2000; 7 (4): 263-264
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Lynch, S. R., Recht, M. I., Puglisi, J. D. Biochemical and nuclear magnetic resonance studies of aminoglycoside-RNA complexes RNA-LIGAND INTERACTIONS PT A, 2000; 317: 240-261
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Puglisi, J. D., Blanchard, S. C., Dahlquist, K. D., Eason, R. G., Fourmy, D., Lynch, S. R., Recht, M. I., Yoshizawa, S. Aminoglycoside antibiotics and decoding International Ribosome Conference, AMER SOC MICROBIOLOGY. 2000: 419–429
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1999
Green, R., Puglisi, J. D. The ribosome revealed NATURE STRUCTURAL BIOLOGY, 1999;
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Yoshizawa, S., Fourmy, D., Puglisi, J. D. Recognition of the codon-anticodon helix by ribosomal RNA SCIENCE, 1999; 285 (5434): 1722-1725
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Recht, M. I., Douthwaite, S., Puglisi, J. D. Basis for prokaryotic specificity of action of aminoglycoside antibiotics EMBO JOURNAL, 1999; 18 (11): 3133-3138
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Recht, M. I., Douthwaite, S., Dahlquist, K. D., Puglisi, J. D. Effect of mutations in the A site of 16S rRNA on aminoglycoside antibiotic-ribosome interaction JOURNAL OF MOLECULAR BIOLOGY, 1999; 286 (1): 33-43
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Puglisi JD, Williamson JR RNA Interaction with Small Ligands and Peptides The RNA World, 2nd Ed.: The Nature of Modern RNA Suggests a Prebiotic RNA World, 1999; 37: 403-425
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Puglisi JD, Blanchard SC, Dahlquist KD, Eason RG, Fourmy D, Lynch SR, Recht MI, Yoshizawa S Structural basis for aminoglycoside antibiotic action Ribosomes, 1999; Ch 34: 419-29
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1998
Puglisi, E. V., Puglisi, J. D. HIV-1 A-rich RNA loop mimics the tRNA anticodon structure NATURE STRUCTURAL BIOLOGY, 1998; 5 (12): 1033-1036
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Yoshizawa, S., Fourmy, D., Puglisi, J. D. Structural origins of gentamicin antibiotic action EMBO JOURNAL, 1998; 17 (22): 6437-6448
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Blanchard, S. C., Fourmy, D., Eason, R. G., Puglisi, J. D. rRNA chemical groups required for aminoglycoside binding BIOCHEMISTRY, 1998; 37 (21): 7716-7724
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Fourmy, D., Recht, M. I., Puglisi, J. D. Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA JOURNAL OF MOLECULAR BIOLOGY, 1998; 277 (2): 347-362
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Fourmy, D., Yoshizawa, S., Puglisi, J. D. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA JOURNAL OF MOLECULAR BIOLOGY, 1998; 277 (2): 333-345
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Puglisi EV, and Puglisi JD Nuclear magnetic resonance spectroscopy of RNA CSHL Press (In RNA Structure and Function, (Symons, R. W., and Grunberg-Manago, M., eds), 1998: 117-46
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Yoshizawa, S., Puglisi, J. D. NMR structure determination of an antibiotic-RNA complex NATO Advanced Study Institute and International School of Structural Biology and Magnetic Resonance, 3rd Course on Protein Dynamics. Function, and Design, PLENUM PRESS DIV PLENUM PUBLISHING CORP. 1998: 173–182
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1997
Puglisi, E. V., Green, R., Noller, H. F., Puglisi, J. D. Structure of a conserved RNA component of the peptidyl transferase centre NATURE STRUCTURAL BIOLOGY, 1997; 4 (10): 775-778
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Puglisi JD Structural basis for aminoglycoside antibiotic action Many Faces of RNA, 1997: 97-111
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1996
Fourmy, D., Recht, M. I., Blanchard, S. C., Puglisi, J. D. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic SCIENCE, 1996; 274 (5291): 1367-1371
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Recht, M. I., Fourmy, D., Blanchard, S. C., Dahlquist, K. D., Puglisi, J. D. RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide JOURNAL OF MOLECULAR BIOLOGY, 1996; 262 (4): 421-436
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1995
Puglisi, J. D., Chen, L., Blanchard, S., Frankel, A. D. SOLUTION STRUCTURE OF A BOVINE IMMUNODEFICIENCY VIRUS TAT-TAR PEPTIDE-RNA COMPLEX SCIENCE, 1995; 270 (5239): 1200-1203
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Puglisi, J. D., Wyatt, J. R. Biochemical and NMR studies of RNA conformation with an emphasis on RNA pseudoknots NUCLEAR MAGNETIC RESONANCE AND NUCLEIC ACIDS, 1995; 261: 323-350
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Puglisi JD Welcome guests to the RNA World: Proteins that interact with RNA Chemistry and Biology, 1995; 2: 581
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Dahlquist, K., Puglisi, J. D. Investigating the structure and function of translation initiation factor 1 in Escherichia coli. Nucleic acids symposium series, 1995: 170-171
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1994
Puglisi, E. V., Puglisi, J. D., Williamson, J. R., RajBhandary, U. L. NMR ANALYSIS OF TRANSFER-RNA ACCEPTOR STEM MICROHELICES - DISCRIMINATOR BASE CHANGE AFFECTS TRANSFER-RNA CONFORMATION AT THE 3' END PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994; 91 (24): 11467-11471
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Puglisi, J. D., Williamson, J. R. NMR-STUDIES OF HIV TAR RNA 8th Conversation in the Discipline Biomolecular Stereodynamics, ADENINE PRESS. 1994: 285–291
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1993
Putz, J., Puglisi, J. D., Florentz, C., Giege, R. ADDITIVE, COOPERATIVE AND ANTI-COOPERATIVE EFFECTS BETWEEN IDENTITY NUCLEOTIDES OF A TRANSFER-RNA EMBO JOURNAL, 1993; 12 (7): 2949-2957
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Puglisi, J. D., Chen, L., Frankel, A. D., Williamson, J. R. ROLE OF RNA STRUCTURE IN ARGININE RECOGNITION OF TAR RNA PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1993; 90 (8): 3680-3684
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Puglisi, J. D., Putz, J., Florentz, C., Giege, R. INFLUENCE OF TRANSFER-RNA TERTIARY STRUCTURE AND STABILITY ON AMINOACYLATION BY YEAST ASPARTYL-TRANSFER RNA-SYNTHETASE NUCLEIC ACIDS RESEARCH, 1993; 21 (1): 41-49
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Giege, R., Puglisi, J. D., Florentz, C. TRANSFER-RNA STRUCTURE AND AMINOACYLATION EFFICIENCY PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY, VOL 45, 1993; 45: 129-206
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1992
Batey, R. T., Inada, M., Kujawinski, E., Puglisi, J. D., Williamson, J. R. PREPARATION OF ISOTOPICALLY LABELED RIBONUCLEOTIDES FOR MULTIDIMENSIONAL NMR-SPECTROSCOPY OF RNA NUCLEIC ACIDS RESEARCH, 1992; 20 (17): 4515-4523
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Perret, V., Florentz, C., Puglisi, J. D., Giege, R. EFFECT OF CONFORMATIONAL FEATURES ON THE AMINOACYLATION OF TRANSFER-RNAS AND CONSEQUENCES ON THE PERMUTATION OF TRANSFER-RNA SPECIFICITIES JOURNAL OF MOLECULAR BIOLOGY, 1992; 226 (2): 323-333
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Puglisi, J. D., Tan, R. Y., CALNAN, B. J., Frankel, A. D., Williamson, J. R. CONFORMATION OF THE TAR RNA-ARGININE COMPLEX BY NMR-SPECTROSCOPY SCIENCE, 1992; 257 (5066): 76-80
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Rudinger, J., Puglisi, J. D., Putz, J., Schatz, D., Eckstein, F., Florentz, C., Giege, R. DETERMINANT NUCLEOTIDES OF YEAST TRANSFER RNA(ASP) INTERACT DIRECTLY WITH ASPARTYL-TRANSFER RNA-SYNTHETASE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992; 89 (13): 5882-5886
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Puglisi JD, Tan R, Frankel AD, Williamson JR Structure and Function of HIV TAR RNA Advances in Life Sciences, (In Structural Tools for the Analysis of Protein-Nucleic Acid Complexes, D Lilley, H Heumann, D Suck, ed.)., 1992: 269-85
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1991
Wyatt, J. R., Chastain, M., Puglisi, J. D. SYNTHESIS AND PURIFICATION OF LARGE AMOUNTS OF RNA OLIGONUCLEOTIDES BIOTECHNIQUES, 1991; 11 (6): 764-769
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Putz, J., Puglisi, J. D., Florentz, C., Giege, R. IDENTITY ELEMENTS FOR SPECIFIC AMINOACYLATION OF YEAST TRANSFER RNAASP BY COGNATE ASPARTYL-TRANSFER RNA-SYNTHETASE SCIENCE, 1991; 252 (5013): 1696-1699
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Puglisi, J. D., Wyatt, J. R., Tinoco, I. RNA PSEUDOKNOTS ACCOUNTS OF CHEMICAL RESEARCH, 1991; 24 (5): 152-158
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1990
Perret, V., Garcia, A., Puglisi, J., Grosjean, H., Ebel, J. P., Florentz, C., Giege, R. CONFORMATION IN SOLUTION OF YEAST TRANSFER RNAASP TRANSCRIPTS DEPRIVED OF MODIFIED NUCLEOTIDES BIOCHIMIE, 1990; 72 (10): 735-744
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Puglisi, J. D., Wyatt, J. R., Tinoco, I. CONFORMATION OF AN RNA PSEUDOKNOT JOURNAL OF MOLECULAR BIOLOGY, 1990; 214 (2): 437-453
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Wyatt, J. R., Puglisi, J. D., Tinoco, I. RNA PSEUDOKNOTS - STABILITY AND LOOP SIZE REQUIREMENTS JOURNAL OF MOLECULAR BIOLOGY, 1990; 214 (2): 455-470
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Giege, R., Florentz, C., Garcia, A., Grosjean, H., Perret, V., Puglisi, J., THEOBALDDIETRICH, A., Ebel, J. P. EXPLORING THE AMINOACYLATION FUNCTION OF TRANSFER-RNA BY MACROMOLECULAR ENGINEERING APPROACHES - INVOLVEMENT OF CONFORMATIONAL FEATURES IN THE CHARGING PROCESS OF YEAST TRANSFER RNAASP BIOCHIMIE, 1990; 72 (6-7): 453-461
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Puglisi, J. D., Wyatt, J. R., Tinoco, I. SOLUTION CONFORMATION OF AN RNA HAIRPIN LOOP BIOCHEMISTRY, 1990; 29 (17): 4215-4226
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1989
Wyatt, J. R., Puglisi, J. D., Tinoco, I. RNA FOLDING - PSEUDOKNOTS, LOOPS AND BULGES BIOESSAYS, 1989; 11 (4): 100-106
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Puglisi, J. D., Tinoco, I. ABSORBENCY MELTING CURVES OF RNA METHODS IN ENZYMOLOGY, 1989; 180: 304-325
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Tinoco I Jr, Aboul-ela F, Hardin CC, Puglisi JD, Varani G, Walker GT, Wolk S, Wyatt JR Nucleic Acids from A to Z Blackwell Scientific Publications, Oxford (In Frontiers of Macromolecular Science, (T Saegusa, T Higashimura and A Abe, eds.)., 1989: 519-24
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1988
Puglisi, J. D., Wyatt, J. R., Tinoco, I. A PSEUDOKNOTTED RNA OLIGONUCLEOTIDE NATURE, 1988; 331 (6153): 283-286
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Wyatt JR, Puglisi JD, Tinoco I Jr Pseudoknotted RNA Oligonucleotides UCLA Symposia Series, Alan R Liss Inc, New York, NY (In Molecular Biology of RNA, T. Cech, ed.), 1988; 94: 25-32
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1987
Trulson, M. O., Cruz, P., Puglisi, J. D., Tinoco, I., Mathies, R. A. RAMAN-SPECTROSCOPIC STUDY OF LEFT-HANDED Z-RNA BIOCHEMISTRY, 1987; 26 (26): 8624-8630
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Hardin, C. C., Zarling, D. A., Puglisi, J. D., Trulson, M. O., Davis, P. W., Tinoco, I. STABILIZATION OF Z-RNA BY CHEMICAL BROMINATION AND ITS RECOGNITION BY ANTI-Z-DNA ANTIBODIES BIOCHEMISTRY, 1987; 26 (16): 5191-5199
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Tinoco, I., Davis, P. W., Hardin, C. C., Puglisi, J. D., Walker, G. T., Wyatt, J. RNA STRUCTURE FROM A TO Z COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY, 1987; 52: 135-146
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1986
Cruz P, Hall K, Puglisi JD, Davis P, Hardin C, Trulson M, Mathies R, Tinoco, I , Jr, Johnson W Jr, Neilson T The Left-Handed Z-Form of Double-Stranded RNA Adenine Press, New York (In Biomolecular Stereodynamics, IV), 1986: 179-200
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Tinoco I Jr., Cruz P, Davis P, Hall K, Hardin CC, Mathies RA, Puglisi JD, Trulson MO, Johnson WC, Neilson T Z-RNA: A Left-Handed Double Helix Plenum Press (In Structure and Dynamics of RNA), 1986: 55-68
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