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Items: 1 to 50 of 145


Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.

Roh JH, Kilburn D, Behrouzi R, Sung W, Briber RM, Woodson SA.

J Phys Chem Lett. 2018 Oct 4;9(19):5726-5732. doi: 10.1021/acs.jpclett.8b02086. Epub 2018 Sep 18.


Mimicking Co-Transcriptional RNA Folding Using a Superhelicase.

Hua B, Panja S, Wang Y, Woodson SA, Ha T.

J Am Chem Soc. 2018 Aug 15;140(32):10067-10070. doi: 10.1021/jacs.8b03784. Epub 2018 Aug 3.


Proteins That Chaperone RNA Regulation.

Woodson SA, Panja S, Santiago-Frangos A.

Microbiol Spectr. 2018 Jul;6(4). doi: 10.1128/microbiolspec.RWR-0026-2018.


Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays.

Hao Y, Bohon J, Hulscher R, Rappé MC, Gupta S, Adilakshmi T, Woodson SA.

Curr Protoc Nucleic Acid Chem. 2018 Jun;73(1):e52. doi: 10.1002/cpnc.52. Epub 2018 Jun 7.


A metastable rRNA junction essential for bacterial 30S biogenesis.

Sharma IM, Rappé MC, Addepalli B, Grabow WW, Zhuang Z, Abeysirigunawardena SC, Limbach PA, Jaeger L, Woodson SA.

Nucleic Acids Res. 2018 Jun 1;46(10):5182-5194. doi: 10.1093/nar/gky120.


The Hfq chaperone helps the ribosome mature.

Sharma IM, Korman A, Woodson SA.

EMBO J. 2018 Jun 1;37(11). pii: e99616. doi: 10.15252/embj.201899616. Epub 2018 May 15. No abstract available.


Hfq chaperone brings speed dating to bacterial sRNA.

Santiago-Frangos A, Woodson SA.

Wiley Interdiscip Rev RNA. 2018 Jul;9(4):e1475. doi: 10.1002/wrna.1475. Epub 2018 Apr 6. Review.


The Pseudomonas aeruginosa PrrF1 and PrrF2 Small Regulatory RNAs Promote 2-Alkyl-4-Quinolone Production through Redundant Regulation of the antR mRNA.

Djapgne L, Panja S, Brewer LK, Gans JH, Kane MA, Woodson SA, Oglesby-Sherrouse AG.

J Bacteriol. 2018 Apr 24;200(10). pii: e00704-17. doi: 10.1128/JB.00704-17. Print 2018 May 15.


Probing RNA Folding Pathways by RNA Fingerprinting.

Woodson SA.

Curr Protoc Nucleic Acid Chem. 2017 Sep 18;70:11.4.1-11.4.19. doi: 10.1002/cpnc.36.


Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes.

Abeysirigunawardena SC, Kim H, Lai J, Ragunathan K, Rappé MC, Luthey-Schulten Z, Ha T, Woodson SA.

Nat Commun. 2017 Sep 8;8(1):492. doi: 10.1038/s41467-017-00536-1.


Acidic C-terminal domains autoregulate the RNA chaperone Hfq.

Santiago-Frangos A, Jeliazkov JR, Gray JJ, Woodson SA.

Elife. 2017 Aug 9;6. pii: e27049. doi: 10.7554/eLife.27049.


Metals induce transient folding and activation of the twister ribozyme.

Panja S, Hua B, Zegarra D, Ha T, Woodson SA.

Nat Chem Biol. 2017 Oct;13(10):1109-1114. doi: 10.1038/nchembio.2459. Epub 2017 Aug 21.


Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.

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, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferré-D'Amaré AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA, Wang YX.

Nature. 2017 Jan 12;541(7636):242-246. doi: 10.1038/nature20599. Epub 2016 Nov 14.


Entropic stabilization of folded RNA in crowded solutions measured by SAXS.

Kilburn D, Behrouzi R, Lee HT, Sarkar K, Briber RM, Woodson SA.

Nucleic Acids Res. 2016 Nov 2;44(19):9452-9461. Epub 2016 Jul 4.


C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA.

Santiago-Frangos A, Kavita K, Schu DJ, Gottesman S, Woodson SA.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6089-E6096. Epub 2016 Sep 28.


Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria.

Zheng A, Panja S, Woodson SA.

J Mol Biol. 2016 Jun 5;428(11):2259-2264. doi: 10.1016/j.jmb.2016.03.027. Epub 2016 Apr 2.


Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.

Hulscher RM, Bohon J, Rappé MC, Gupta S, D'Mello R, Sullivan M, Ralston CY, Chance MR, Woodson SA.

Methods. 2016 Jul 1;103:49-56. doi: 10.1016/j.ymeth.2016.03.012. Epub 2016 Mar 22.


Charge screening in RNA: an integral route for dynamical enhancements.

Roh JH, Tyagi M, Aich P, Kim K, Briber RM, Woodson SA.

Soft Matter. 2015 Dec 7;11(45):8741-5. doi: 10.1039/c5sm02084k.


Differential effects of ribosomal proteins and Mg2+ ions on a conformational switch during 30S ribosome 5'-domain assembly.

Abeysirigunawardena SC, Woodson SA.

RNA. 2015 Nov;21(11):1859-65. doi: 10.1261/rna.051292.115. Epub 2015 Sep 9.


Acidic Residues in the Hfq Chaperone Increase the Selectivity of sRNA Binding and Annealing.

Panja S, Santiago-Frangos A, Schu DJ, Gottesman S, Woodson SA.

J Mol Biol. 2015 Nov 6;427(22):3491-3500. doi: 10.1016/j.jmb.2015.07.010. Epub 2015 Jul 18.


Preface. Structures of Large RNA Molecules and Their Complexes.

Allain FH, Woodson SA.

Methods Enzymol. 2015;558:xix-xxi. doi: 10.1016/S0076-6879(15)00322-5. No abstract available.


Light-Triggered RNA Annealing by an RNA Chaperone.

Panja S, Paul R, Greenberg MM, Woodson SA.

Angew Chem Int Ed Engl. 2015 Jun 15;54(25):7281-4. doi: 10.1002/anie.201501658. Epub 2015 May 8.


RNA folding retrospective: lessons from ribozymes big and small.

Woodson SA.

RNA. 2015 Apr;21(4):502-3. doi: 10.1261/rna.051110.115. No abstract available.


Fluorescence reporters for Hfq oligomerization and RNA annealing.

Panja S, Woodson SA.

Methods Mol Biol. 2015;1259:369-83. doi: 10.1007/978-1-4939-2214-7_22.


Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme.

Lee HT, Kilburn D, Behrouzi R, Briber RM, Woodson SA.

Nucleic Acids Res. 2015 Jan;43(2):1170-6. doi: 10.1093/nar/gku1335. Epub 2014 Dec 24.


Structural model of an mRNA in complex with the bacterial chaperone Hfq.

Peng Y, Curtis JE, Fang X, Woodson SA.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17134-9. doi: 10.1073/pnas.1410114111. Epub 2014 Nov 17.


An improved surface passivation method for single-molecule studies.

Hua B, Han KY, Zhou R, Kim H, Shi X, Abeysirigunawardena SC, Jain A, Singh D, Aggarwal V, Woodson SA, Ha T.

Nat Methods. 2014 Dec;11(12):1233-6. doi: 10.1038/nmeth.3143. Epub 2014 Oct 12.


Protein-guided RNA dynamics during early ribosome assembly.

Kim H, Abeysirigunawarden SC, Chen K, Mayerle M, Ragunathan K, Luthey-Schulten Z, Ha T, Woodson SA.

Nature. 2014 Feb 20;506(7488):334-8. doi: 10.1038/nature13039. Epub 2014 Feb 12.


Increased ribozyme activity in crowded solutions.

Desai R, Kilburn D, Lee HT, Woodson SA.

J Biol Chem. 2014 Jan 31;289(5):2972-7. doi: 10.1074/jbc.M113.527861. Epub 2013 Dec 11.


In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates.

Clatterbuck Soper SF, Dator RP, Limbach PA, Woodson SA.

Mol Cell. 2013 Nov 21;52(4):506-16. doi: 10.1016/j.molcel.2013.09.020. Epub 2013 Oct 24.


Positional effects of AAN motifs in rpoS regulation by sRNAs and Hfq.

Peng Y, Soper TJ, Woodson SA.

J Mol Biol. 2014 Jan 23;426(2):275-85. doi: 10.1016/j.jmb.2013.08.026. Epub 2013 Sep 16.


Biopolymers celebrates 50 years of nucleic acids research.

Breslauer KJ, Case DA, Walter NG, Woodson SA.

Biopolymers. 2013 Dec;99(12):909. doi: 10.1002/bip.22358. No abstract available.


Crowders perturb the entropy of RNA energy landscapes to favor folding.

Kilburn D, Roh JH, Behrouzi R, Briber RM, Woodson SA.

J Am Chem Soc. 2013 Jul 10;135(27):10055-63. doi: 10.1021/ja4030098. Epub 2013 Jul 1.


Conserved arginines on the rim of Hfq catalyze base pair formation and exchange.

Panja S, Schu DJ, Woodson SA.

Nucleic Acids Res. 2013 Aug;41(15):7536-46. doi: 10.1093/nar/gkt521. Epub 2013 Jun 14.


Specific contacts between protein S4 and ribosomal RNA are required at multiple stages of ribosome assembly.

Mayerle M, Woodson SA.

RNA. 2013 Apr;19(4):574-85. doi: 10.1261/rna.037028.112. Epub 2013 Feb 21.


Hfq proximity and orientation controls RNA annealing.

Panja S, Woodson SA.

Nucleic Acids Res. 2012 Sep 1;40(17):8690-7. Epub 2012 Jul 2.


RNase footprinting of protein binding sites on an mRNA target of small RNAs.

Peng Y, Soper TJ, Woodson SA.

Methods Mol Biol. 2012;905:213-24. doi: 10.1007/978-1-61779-949-5_13.


Rendering RNA in 3D.

Behrouzi R, Woodson SA.

Nat Methods. 2012 May 30;9(6):552-3. doi: 10.1038/nmeth.2045. No abstract available.


Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures.

Koculi E, Cho SS, Desai R, Thirumalai D, Woodson SA.

Nucleic Acids Res. 2012 Sep;40(16):8011-20. doi: 10.1093/nar/gks468. Epub 2012 May 28.


Cooperative tertiary interaction network guides RNA folding.

Behrouzi R, Roh JH, Kilburn D, Briber RM, Woodson SA.

Cell. 2012 Apr 13;149(2):348-57. doi: 10.1016/j.cell.2012.01.057.


Hexamer to monomer equilibrium of E. coli Hfq in solution and its impact on RNA annealing.

Panja S, Woodson SA.

J Mol Biol. 2012 Apr 13;417(5):406-12. doi: 10.1016/j.jmb.2012.02.009. Epub 2012 Feb 10.


The dynamics of unfolded versus folded tRNA: the role of electrostatic interactions.

Roh JH, Tyagi M, Briber RM, Woodson SA, Sokolov AP.

J Am Chem Soc. 2011 Oct 19;133(41):16406-9. doi: 10.1021/ja207667u. Epub 2011 Sep 27.


Slow formation of stable complexes during coincubation of minimal rRNA and ribosomal protein S4.

Mayerle M, Bellur DL, Woodson SA.

J Mol Biol. 2011 Sep 23;412(3):453-65. doi: 10.1016/j.jmb.2011.07.048. Epub 2011 Jul 29.


RNA folding pathways and the self-assembly of ribosomes.

Woodson SA.

Acc Chem Res. 2011 Dec 20;44(12):1312-9. doi: 10.1021/ar2000474. Epub 2011 Jun 29.


Major role for mRNA binding and restructuring in sRNA recruitment by Hfq.

Soper TJ, Doxzen K, Woodson SA.

RNA. 2011 Aug;17(8):1544-50. doi: 10.1261/rna.2767211. Epub 2011 Jun 24.


New era of molecular structure and dynamics from solution scattering experiments.

Sosnick TR, Woodson SA.

Biopolymers. 2011 Aug;95(8):503-4. doi: 10.1002/bip.21643. No abstract available.


Rapid binding and release of Hfq from ternary complexes during RNA annealing.

Hopkins JF, Panja S, Woodson SA.

Nucleic Acids Res. 2011 Jul;39(12):5193-202. doi: 10.1093/nar/gkr062. Epub 2011 Mar 4.


Taming free energy landscapes with RNA chaperones.

Woodson SA.

RNA Biol. 2010 Nov-Dec;7(6):677-86. Epub 2010 Nov 1. Review.


Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering.

Roh JH, Guo L, Kilburn JD, Briber RM, Irving T, Woodson SA.

J Am Chem Soc. 2010 Jul 28;132(29):10148-54. doi: 10.1021/ja103867p.


Molecular crowding stabilizes folded RNA structure by the excluded volume effect.

Kilburn D, Roh JH, Guo L, Briber RM, Woodson SA.

J Am Chem Soc. 2010 Jun 30;132(25):8690-6. doi: 10.1021/ja101500g.

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