Literature DB >> 35659535

How does RNA fold dynamically?

David Z Bushhouse1, Edric K Choi2, Laura M Hertz3, Julius B Lucks4.   

Abstract

Recent advances in interrogating RNA folding dynamics have shown the classical model of RNA folding to be incomplete. Here, we pose three prominent questions for the field that are at the forefront of our understanding of the importance of RNA folding dynamics for RNA function. The first centers on the most appropriate biophysical framework to describe changes to the RNA folding energy landscape that a growing RNA chain encounters during transcriptional elongation. The second focuses on the potential ubiquity of strand displacement - a process by which RNA can rapidly change conformations - and how this process may be generally present in broad classes of seemingly different RNAs. The third raises questions about the potential importance and roles of cellular protein factors in RNA conformational switching. Answers to these questions will greatly improve our fundamental knowledge of RNA folding and function, drive biotechnological advances that utilize engineered RNAs, and potentially point to new areas of biology yet to be discovered.
Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Entities:  

Keywords:  conformational switching; cotranscriptional RNA folding; energy landscapes; protein-mediated RNA folding; strand displacement

Mesh:

Substances:

Year:  2022        PMID: 35659535      PMCID: PMC9474645          DOI: 10.1016/j.jmb.2022.167665

Source DB:  PubMed          Journal:  J Mol Biol        ISSN: 0022-2836            Impact factor:   6.151


  102 in total

1.  Rearrangement of structured RNA via branch migration structures catalysed by the highly related DEAD-box proteins p68 and p72.

Authors:  O G Rössler; A Straka; H Stahl
Journal:  Nucleic Acids Res       Date:  2001-05-15       Impact factor: 16.971

Review 2.  How RNA folds.

Authors:  I Tinoco; C Bustamante
Journal:  J Mol Biol       Date:  1999-10-22       Impact factor: 5.469

Review 3.  Taming free energy landscapes with RNA chaperones.

Authors:  Sarah A Woodson
Journal:  RNA Biol       Date:  2010-11-01       Impact factor: 4.652

4.  Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures.

Authors:  Terrence N Wong; Tobin R Sosnick; Tao Pan
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-06       Impact factor: 11.205

5.  Structure of a transcribing RNA polymerase II-U1 snRNP complex.

Authors:  Suyang Zhang; Shintaro Aibara; Seychelle M Vos; Dmitry E Agafonov; Reinhard Lührmann; Patrick Cramer
Journal:  Science       Date:  2021-01-15       Impact factor: 47.728

6.  Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing.

Authors:  Julia R Widom; Yuri A Nedialkov; Victoria Rai; Ryan L Hayes; Charles L Brooks; Irina Artsimovitch; Nils G Walter
Journal:  Mol Cell       Date:  2018-11-01       Impact factor: 17.970

7.  Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA.

Authors:  A A Antson; E J Dodson; G Dodson; R B Greaves; X Chen; P Gollnick
Journal:  Nature       Date:  1999-09-16       Impact factor: 49.962

8.  Gene regulation by substoichiometric heterocomplex formation of undecameric TRAP and trimeric anti-TRAP.

Authors:  Elihu C Ihms; Mowei Zhou; Yun Zhang; Ian R Kleckner; Craig A McElroy; Vicki H Wysocki; Paul Gollnick; Mark P Foster
Journal:  Proc Natl Acad Sci U S A       Date:  2014-02-18       Impact factor: 11.205

9.  Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.

Authors:  Daniel Krochmal; Yaming Shao; Nan-Sheng Li; Saurja DasGupta; Sandip A Shelke; Deepak Koirala; Joseph A Piccirilli
Journal:  Nat Chem Biol       Date:  2022-01-20       Impact factor: 16.174

10.  Cotranscriptional folding of a riboswitch at nucleotide resolution.

Authors:  Kyle E Watters; Eric J Strobel; Angela M Yu; John T Lis; Julius B Lucks
Journal:  Nat Struct Mol Biol       Date:  2016-10-31       Impact factor: 15.369

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  1 in total

1.  Regulatory Mechanisms through RNA Conformational Switching and Dynamics.

Authors:  Philip C Bevilacqua; Blanton S Tolbert
Journal:  J Mol Biol       Date:  2022-08-18       Impact factor: 6.151

  1 in total

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