Literature DB >> 18547802

RNA dynamics: it is about time.

Hashim M Al-Hashimi1, Nils G Walter.   

Abstract

Many recently discovered RNA functions rely on highly complex multistep conformational transitions that occur in response to an array of cellular signals. These dynamics accompany and guide, for example, RNA cotranscriptional folding, ligand sensing and signaling, site-specific catalysis in ribozymes, and the hierarchically ordered assembly of ribonucleoproteins. RNA dynamics are encoded by both the inherent properties of RNA structure, spanning many motional modes with a large range of amplitudes and timescales, and external trigger factors, ranging from proteins, nucleic acids, metal ions, metabolites, and vitamins to temperature and even directional RNA biosynthesis itself. Here, we review recent advances in our understanding of RNA dynamics as highlighted by biophysical tools.

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Year:  2008        PMID: 18547802      PMCID: PMC2580758          DOI: 10.1016/j.sbi.2008.04.004

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  50 in total

Review 1.  Self-induced structural switches in RNA.

Authors:  Jord H A Nagel; Cornelis W A Pleij
Journal:  Biochimie       Date:  2002-09       Impact factor: 4.079

2.  Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance.

Authors:  David Rueda; Gregory Bokinsky; Maria M Rhodes; Michael J Rust; Xiaowei Zhuang; Nils G Walter
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-24       Impact factor: 11.205

Review 3.  Riboswitches as versatile gene control elements.

Authors:  Brian J Tucker; Ronald R Breaker
Journal:  Curr Opin Struct Biol       Date:  2005-06       Impact factor: 6.809

4.  An assembly landscape for the 30S ribosomal subunit.

Authors:  Megan W T Talkington; Gary Siuzdak; James R Williamson
Journal:  Nature       Date:  2005-12-01       Impact factor: 49.962

Review 5.  The regulatory roles and mechanism of transcriptional pausing.

Authors:  R Landick
Journal:  Biochem Soc Trans       Date:  2006-12       Impact factor: 5.407

6.  Binding of U1A protein changes RNA dynamics as observed by 13C NMR relaxation studies.

Authors:  Zahra Shajani; Gary Drobny; Gabriele Varani
Journal:  Biochemistry       Date:  2007-05-01       Impact factor: 3.162

7.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.

Authors:  Wade Winkler; Ali Nahvi; Ronald R Breaker
Journal:  Nature       Date:  2002-10-16       Impact factor: 49.962

8.  The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.

Authors:  J Kenneth Wickiser; Wade C Winkler; Ronald R Breaker; Donald M Crothers
Journal:  Mol Cell       Date:  2005-04-01       Impact factor: 17.970

9.  A threefold RNA-protein interface in the signal recognition particle gates native complex assembly.

Authors:  Tuhin Subhra Maity; Kevin M Weeks
Journal:  J Mol Biol       Date:  2007-03-20       Impact factor: 5.469

10.  The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis.

Authors:  Jana Sefcikova; Maryna V Krasovska; Jirí Sponer; Nils G Walter
Journal:  Nucleic Acids Res       Date:  2007-03-02       Impact factor: 16.971

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  126 in total

Review 1.  RNA Structural Differentiation: Opportunities with Pattern Recognition.

Authors:  Christopher S Eubanks; Amanda E Hargrove
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

Review 2.  Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology.

Authors:  Nicole Michelotti; Alexander Johnson-Buck; Anthony J Manzo; Nils G Walter
Journal:  Wiley Interdiscip Rev Nanomed Nanobiotechnol       Date:  2011-11-30

3.  RNA structure: Adding a second dimension.

Authors:  Katja Petzold; Hashim M Al-Hashimi
Journal:  Nat Chem       Date:  2011-11-23       Impact factor: 24.427

4.  Thermodynamics of RNA melting, one base pair at a time.

Authors:  Evgenia N Nikolova; Hashim M Al-Hashimi
Journal:  RNA       Date:  2010-07-21       Impact factor: 4.942

5.  Folding of a transcriptionally acting preQ1 riboswitch.

Authors:  Ulrike Rieder; Christoph Kreutz; Ronald Micura
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-01       Impact factor: 11.205

6.  Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling.

Authors:  Xiaojun Zhang; Sang Won Lee; Liang Zhao; Tianbing Xia; Peter Z Qin
Journal:  RNA       Date:  2010-10-27       Impact factor: 4.942

7.  Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations.

Authors:  S Elizabeth McDowell; Jesse M Jun; Nils G Walter
Journal:  RNA       Date:  2010-10-04       Impact factor: 4.942

8.  Mapping L1 ligase ribozyme conformational switch.

Authors:  George M Giambaşu; Tai-Sung Lee; William G Scott; Darrin M York
Journal:  J Mol Biol       Date:  2012-07-03       Impact factor: 5.469

Review 9.  Themes and variations in riboswitch structure and function.

Authors:  Alla Peselis; Alexander Serganov
Journal:  Biochim Biophys Acta       Date:  2014-02-28

10.  Methyl transfer by substrate signaling from a knotted protein fold.

Authors:  Thomas Christian; Reiko Sakaguchi; Agata P Perlinska; Georges Lahoud; Takuhiro Ito; Erika A Taylor; Shigeyuki Yokoyama; Joanna I Sulkowska; Ya-Ming Hou
Journal:  Nat Struct Mol Biol       Date:  2016-08-29       Impact factor: 15.369

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