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Relating Structure and Dynamics in RNA Biology.

Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD.

Cold Spring Harb Perspect Biol. 2019 Jul 1;11(7). pii: a032474. doi: 10.1101/cshperspect.a032474. Review.


Expanding single-molecule fluorescence spectroscopy to capture complexity in biology.

Choi J, Grosely R, Puglisi EV, Puglisi JD.

Curr Opin Struct Biol. 2019 Jun 15. pii: S0959-440X(18)30129-5. doi: 10.1016/ [Epub ahead of print] Review.


RACK1 on and off the ribosome.

Johnson AG, Lapointe CP, Wang J, Corsepius NC, Choi J, Fuchs G, Puglisi JD.

RNA. 2019 Jul;25(7):881-895. doi: 10.1261/rna.071217.119. Epub 2019 Apr 25.


Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts.

Duss O, Stepanyuk GA, Grot A, O'Leary SE, Puglisi JD, Williamson JR.

Nat Commun. 2018 Nov 30;9(1):5087. doi: 10.1038/s41467-018-07423-3.


De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes.

Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R.

Nat Methods. 2018 Nov;15(11):947-954. doi: 10.1038/s41592-018-0172-2. Epub 2018 Oct 30.


Dynamic Interplay of RNA and Protein in the Human Immunodeficiency Virus-1 Reverse Transcription Initiation Complex.

Coey AT, Larsen KP, Choi J, Barrero DJ, Puglisi JD, Puglisi EV.

J Mol Biol. 2018 Dec 7;430(24):5137-5150. doi: 10.1016/j.jmb.2018.08.029. Epub 2018 Sep 7.


How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation.

Choi J, Grosely R, Prabhakar A, Lapointe CP, Wang J, Puglisi JD.

Annu Rev Biochem. 2018 Jun 20;87:421-449. doi: 10.1146/annurev-biochem-060815-014818. Review.


Single-Molecule Fluorescence Applied to Translation.

Prabhakar A, Puglisi EV, Puglisi JD.

Cold Spring Harb Perspect Biol. 2019 Jan 2;11(1). pii: a032714. doi: 10.1101/cshperspect.a032714. Review.


Architecture of an HIV-1 reverse transcriptase initiation complex.

Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV.

Nature. 2018 May;557(7703):118-122. doi: 10.1038/s41586-018-0055-9. Epub 2018 Apr 25.


2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD.

Nat Struct Mol Biol. 2018 Mar;25(3):208-216. doi: 10.1038/s41594-018-0030-z. Epub 2018 Feb 19.


Three tRNAs on the ribosome slow translation elongation.

Choi J, Puglisi JD.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13691-13696. doi: 10.1073/pnas.1719592115. Epub 2017 Dec 11.


Fluorescently-tagged human eIF3 for single-molecule spectroscopy.

Johnson AG, Petrov AN, Fuchs G, Majzoub K, Grosely R, Choi J, Puglisi JD.

Nucleic Acids Res. 2018 Jan 25;46(2):e8. doi: 10.1093/nar/gkx1050.


Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling.

Prabhakar A, Capece MC, Petrov A, Choi J, Puglisi JD.

Cell Rep. 2017 Jul 5;20(1):161-172. doi: 10.1016/j.celrep.2017.06.028.


Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination.

Prabhakar A, Choi J, Wang J, Petrov A, Puglisi JD.

Protein Sci. 2017 Jul;26(7):1352-1362. doi: 10.1002/pro.3190. Epub 2017 May 23. Review.


Dynamics of IRES-mediated translation.

Johnson AG, Grosely R, Petrov AN, Puglisi JD.

Philos Trans R Soc Lond B Biol Sci. 2017 Mar 19;372(1716). pii: 20160177. doi: 10.1098/rstb.2016.0177. Review.


The molecular choreography of protein synthesis: translational control, regulation, and pathways.

Chen J, Choi J, O'Leary SE, Prabhakar A, Petrov A, Grosely R, Puglisi EV, Puglisi JD.

Q Rev Biophys. 2016 Jan;49:e11. Epub 2016 Jun 24.


Heterogeneous structures formed by conserved RNA sequences within the HIV reverse transcription initiation site.

Coey A, Larsen K, Puglisi JD, Viani Puglisi E.

RNA. 2016 Nov;22(11):1689-1698. Epub 2016 Sep 9.


Amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences.

Navon SP, Kornberg G, Chen J, Schwartzman T, Tsai A, Puglisi EV, Puglisi JD, Adir N.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7166-70. doi: 10.1073/pnas.1606518113. Epub 2016 Jun 15.


Multiple Parallel Pathways of Translation Initiation on the CrPV IRES.

Petrov A, Grosely R, Chen J, O'Leary SE, Puglisi JD.

Mol Cell. 2016 Apr 7;62(1):92-103. doi: 10.1016/j.molcel.2016.03.020.


Probing the Translation Dynamics of Ribosomes Using Zero-Mode Waveguides.

Tsai A, Puglisi JD, Uemura S.

Prog Mol Biol Transl Sci. 2016;139:1-43. doi: 10.1016/bs.pmbts.2015.10.006. Epub 2015 Nov 2. Review.


N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics.

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.

Nat Struct Mol Biol. 2016 Feb;23(2):110-5. doi: 10.1038/nsmb.3148. Epub 2016 Jan 11.


Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II.

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, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H.

Nat Methods. 2016 Jan;13(1):59-62. doi: 10.1038/nmeth.3667. Epub 2015 Nov 30.


The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer.

Siprashvili Z, Webster DE, Johnston D, Shenoy RM, Ungewickell AJ, Bhaduri A, Flockhart R, Zarnegar BJ, Che Y, Meschi F, Puglisi JD, Khavari PA.

Nat Genet. 2016 Jan;48(1):53-8. doi: 10.1038/ng.3452. Epub 2015 Nov 23.


Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

Chen J, Coakley A, O'Connor M, Petrov A, O'Leary SE, Atkins JF, Puglisi JD.

Cell. 2015 Nov 19;163(5):1267-1280. doi: 10.1016/j.cell.2015.10.064.


Cotranslational Protein Folding inside the Ribosome Exit Tunnel.

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.

Cell Rep. 2015 Sep 8;12(10):1533-40. doi: 10.1016/j.celrep.2015.07.065. Epub 2015 Aug 28.


Synthetic biology: Ribosomal ties that bind.

Puglisi JD.

Nature. 2015 Aug 6;524(7563):45-6. doi: 10.1038/nature14642. Epub 2015 Jul 29. No abstract available.


Protein synthesis. The delicate dance of translation and folding.

Puglisi JD.

Science. 2015 Apr 24;348(6233):399-400. doi: 10.1126/science.aab2157. No abstract available.


RNA dances to center stage.

Puglisi JD.

RNA. 2015 Apr;21(4):712-3. doi: 10.1261/rna.051078.115. No abstract available.


A simple real-time assay for in vitro translation.

Capece MC, Kornberg GL, Petrov A, Puglisi JD.

RNA. 2015 Feb;21(2):296-305. doi: 10.1261/rna.047159.114. Epub 2014 Dec 18.


Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site.

Fuchs G, Petrov AN, Marceau CD, Popov LM, Chen J, O'Leary SE, Wang R, Carette JE, Sarnow P, Puglisi JD.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):319-25. doi: 10.1073/pnas.1421328111. Epub 2014 Dec 16.


Real-time observation of signal recognition particle binding to actively translating ribosomes.

Noriega TR, Chen J, Walter P, Puglisi JD.

Elife. 2014 Oct 30;3. doi: 10.7554/eLife.04418.


Dynamic pathways of -1 translational frameshifting.

Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD.

Nature. 2014 Aug 21;512(7514):328-32. doi: 10.1038/nature13428. Epub 2014 Jun 11.


The dynamics of SecM-induced translational stalling.

Tsai A, Kornberg G, Johansson M, Chen J, Puglisi JD.

Cell Rep. 2014 Jun 12;7(5):1521-1533. doi: 10.1016/j.celrep.2014.04.033. Epub 2014 May 15.


Sequence-dependent elongation dynamics on macrolide-bound ribosomes.

Johansson M, Chen J, Tsai A, Kornberg G, Puglisi JD.

Cell Rep. 2014 Jun 12;7(5):1534-1546. doi: 10.1016/j.celrep.2014.04.034. Epub 2014 May 15.


Signal recognition particle-ribosome binding is sensitive to nascent chain length.

Noriega TR, Tsai A, Elvekrog MM, Petrov A, Neher SB, Chen J, Bradshaw N, Puglisi JD, Walter P.

J Biol Chem. 2014 Jul 11;289(28):19294-305. doi: 10.1074/jbc.M114.563239. Epub 2014 May 7.


High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence.

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.

Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):664-9. doi: 10.1073/pnas.1315735111. Epub 2013 Dec 30.


Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E.

O'Leary SE, Petrov A, Chen J, Puglisi JD.

Structure. 2013 Dec 3;21(12):2197-207. doi: 10.1016/j.str.2013.09.016. Epub 2013 Oct 31.


RNA purification by preparative polyacrylamide gel electrophoresis.

Petrov A, Wu T, Puglisi EV, Puglisi JD.

Methods Enzymol. 2013;530:315-30. doi: 10.1016/B978-0-12-420037-1.00017-8.


Analysis of RNA by analytical polyacrylamide gel electrophoresis.

Petrov A, Tsa A, Puglisi JD.

Methods Enzymol. 2013;530:301-13. doi: 10.1016/B978-0-12-420037-1.00016-6.


Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor.

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.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15656-61. doi: 10.1073/pnas.1309578110. Epub 2013 Sep 12.


Coordinated conformational and compositional dynamics drive ribosome translocation.

Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD.

Nat Struct Mol Biol. 2013 Jun;20(6):718-27. doi: 10.1038/nsmb.2567. Epub 2013 Apr 28.


The impact of aminoglycosides on the dynamics of translation elongation.

Tsai A, Uemura S, Johansson M, Puglisi EV, Marshall RA, Aitken CE, Korlach J, Ehrenberg M, Puglisi JD.

Cell Rep. 2013 Feb 21;3(2):497-508. doi: 10.1016/j.celrep.2013.01.027. Epub 2013 Feb 14.


Unraveling the dynamics of ribosome translocation.

Chen J, Tsai A, O'Leary SE, Petrov A, Puglisi JD.

Curr Opin Struct Biol. 2012 Dec;22(6):804-14. doi: 10.1016/ Epub 2012 Nov 8. Review.


Single-molecule analysis of translational dynamics.

Petrov A, Chen J, O'Leary S, Tsai A, Puglisi JD.

Cold Spring Harb Perspect Biol. 2012 Sep 1;4(9):a011551. doi: 10.1101/cshperspect.a011551. Review.


Precursor directed biosynthesis of an orthogonally functional erythromycin analogue: selectivity in the ribosome macrolide binding pocket.

Harvey CJ, Puglisi JD, Pande VS, Cane DE, Khosla C.

J Am Chem Soc. 2012 Jul 25;134(29):12259-65. doi: 10.1021/ja304682q. Epub 2012 Jul 11.


Heterogeneous pathways and timing of factor departure during translation initiation.

Tsai A, Petrov A, Marshall RA, Korlach J, Uemura S, Puglisi JD.

Nature. 2012 Jul 19;487(7407):390-3. doi: 10.1038/nature11172.


Digging deep into nucleic acid structure and nucleic acid protein recognition.

Puglisi JD, Williamson JR.

Curr Opin Struct Biol. 2012 Jun;22(3):249-50. doi: 10.1016/ Epub 2012 May 24. No abstract available.


Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics.

Chen J, Tsai A, Petrov A, Puglisi JD.

J Am Chem Soc. 2012 Apr 4;134(13):5734-7. doi: 10.1021/ja2119964. Epub 2012 Mar 23.


Initiation factor 2, tRNA, and 50S subunits cooperatively stabilize mRNAs on the ribosome during initiation.

Masuda T, Petrov AN, Iizuka R, Funatsu T, Puglisi JD, Uemura S.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4881-5. doi: 10.1073/pnas.1118452109. Epub 2012 Mar 12.


Secondary structure of the HIV reverse transcription initiation complex by NMR.

Puglisi EV, Puglisi JD.

J Mol Biol. 2011 Jul 29;410(5):863-74. doi: 10.1016/j.jmb.2011.04.024.

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