Literature DB >> 31896543

Alternate RNA Structures.

Marie Teng-Pei Wu1, Victoria D'Souza1.   

Abstract

RNA molecules fold into complex three-dimensional structures that sample alternate conformations ranging from minor differences in tertiary structure dynamics to major differences in secondary structure. This allows them to form entirely different substructures with each population potentially giving rise to a distinct biological outcome. The substructures can be partitioned along an existing energy landscape given a particular static cellular cue or can be shifted in response to dynamic cues such as ligand binding. We review a few key examples of RNA molecules that sample alternate conformations and how these are capitalized on for control of critical regulatory functions.
Copyright © 2020 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2020        PMID: 31896543      PMCID: PMC6942119          DOI: 10.1101/cshperspect.a032425

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  156 in total

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Authors:  Francesca Massi; Eric Johnson; Chunyu Wang; Mark Rance; Arthur G Palmer
Journal:  J Am Chem Soc       Date:  2004-02-25       Impact factor: 15.419

2.  Crystal structure of the lysine riboswitch regulatory mRNA element.

Authors:  Andrew D Garst; Annie Héroux; Robert P Rambo; Robert T Batey
Journal:  J Biol Chem       Date:  2008-07-01       Impact factor: 5.157

3.  A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer.

Authors:  Antje C Wolter; A Katharina Weickhmann; Amir H Nasiri; Katharina Hantke; Oliver Ohlenschläger; Christoph H Wunderlich; Christoph Kreutz; Elke Duchardt-Ferner; Jens Wöhnert
Journal:  Angew Chem Int Ed Engl       Date:  2016-11-25       Impact factor: 15.336

4.  Invisible RNA state dynamically couples distant motifs.

Authors:  Janghyun Lee; Elizabeth A Dethoff; Hashim M Al-Hashimi
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-16       Impact factor: 11.205

5.  A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate.

Authors:  Tyler D Ames; Dmitry A Rodionov; Zasha Weinberg; Ronald R Breaker
Journal:  Chem Biol       Date:  2010-07-30

6.  The nonsense-mediated decay pathway and mutually exclusive expression of alternatively spliced FGFR2IIIb and -IIIc mRNAs.

Authors:  R B Jones; F Wang; Y Luo; C Yu; C Jin; T Suzuki; M Kan; W L McKeehan
Journal:  J Biol Chem       Date:  2000-10-20       Impact factor: 5.157

7.  An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

Authors:  Mohit Chawla; Romina Oliva; Janusz M Bujnicki; Luigi Cavallo
Journal:  Nucleic Acids Res       Date:  2015-06-27       Impact factor: 16.971

8.  First snapshots of the HIV-1 RNA structure in infected cells and in virions.

Authors:  Jean-Christophe Paillart; Markus Dettenhofer; Xiao-Fang Yu; Chantal Ehresmann; Bernard Ehresmann; Roland Marquet
Journal:  J Biol Chem       Date:  2004-09-08       Impact factor: 5.157

9.  Direct observation of hierarchical folding in single riboswitch aptamers.

Authors:  William J Greenleaf; Kirsten L Frieda; Daniel A N Foster; Michael T Woodside; Steven M Block
Journal:  Science       Date:  2008-01-03       Impact factor: 47.728

10.  N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding.

Authors:  Katherine I Zhou; Marc Parisien; Qing Dai; Nian Liu; Luda Diatchenko; Joseph R Sachleben; Tao Pan
Journal:  J Mol Biol       Date:  2015-09-04       Impact factor: 5.469

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  3 in total

1.  R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures.

Authors:  Anita Donlic; Emily G Swanson; Liang-Yuan Chiu; Sarah L Wicks; Aline Umuhire Juru; Zhengguo Cai; Kamillah Kassam; Chris Laudeman; Bilva G Sanaba; Andrew Sugarman; Eunseong Han; Blanton S Tolbert; Amanda E Hargrove
Journal:  ACS Chem Biol       Date:  2022-05-20       Impact factor: 4.634

Review 2.  Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.

Authors:  Katarzyna Taylor; Krzysztof Sobczak
Journal:  Int J Mol Sci       Date:  2020-07-21       Impact factor: 5.923

3.  Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.

Authors:  Shuting Yan; Qiyao Zhu; Swati Jain; Tamar Schlick
Journal:  Res Sq       Date:  2022-01-04
  3 in total

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