Literature DB >> 22337051

Functional complexity and regulation through RNA dynamics.

Elizabeth A Dethoff1, Jeetender Chugh, Anthony M Mustoe, Hashim M Al-Hashimi.   

Abstract

Changes to the conformation of coding and non-coding RNAs form the basis of elements of genetic regulation and provide an important source of complexity, which drives many of the fundamental processes of life. Although the structure of RNA is highly flexible, the underlying dynamics of RNA are robust and are limited to transitions between the few conformations that preserve favourable base-pairing and stacking interactions. The mechanisms by which cellular processes harness the intrinsic dynamic behaviour of RNA and use it within functionally productive pathways are complex. The versatile functions and ease by which it is integrated into a wide variety of genetic circuits and biochemical pathways suggests there is a general and fundamental role for RNA dynamics in cellular processes.

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Year:  2012        PMID: 22337051      PMCID: PMC3320162          DOI: 10.1038/nature10885

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  100 in total

1.  Visualizing spatially correlated dynamics that directs RNA conformational transitions.

Authors:  Qi Zhang; Andrew C Stelzer; Charles K Fisher; Hashim M Al-Hashimi
Journal:  Nature       Date:  2007-12-20       Impact factor: 49.962

2.  Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone.

Authors:  Hari Bhaskaran; Rick Russell
Journal:  Nature       Date:  2007-10-25       Impact factor: 49.962

3.  Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA.

Authors:  Paul J Paukstelis; Jui-Hui Chen; Elaine Chase; Alan M Lambowitz; Barbara L Golden
Journal:  Nature       Date:  2008-01-03       Impact factor: 49.962

4.  Spontaneous intersubunit rotation in single ribosomes.

Authors:  Peter V Cornish; Dmitri N Ermolenko; Harry F Noller; Taekjip Ha
Journal:  Mol Cell       Date:  2008-06-06       Impact factor: 17.970

5.  RNA dynamics: it is about time.

Authors:  Hashim M Al-Hashimi; Nils G Walter
Journal:  Curr Opin Struct Biol       Date:  2008-06-09       Impact factor: 6.809

6.  Toward a more complete view of tRNA biology.

Authors:  Richard Giegé
Journal:  Nat Struct Mol Biol       Date:  2008-10-06       Impact factor: 15.369

7.  Structural basis for translation termination on the 70S ribosome.

Authors:  Martin Laurberg; Haruichi Asahara; Andrei Korostelev; Jianyu Zhu; Sergei Trakhanov; Harry F Noller
Journal:  Nature       Date:  2008-07-02       Impact factor: 49.962

8.  A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release.

Authors:  Beate Schwer
Journal:  Mol Cell       Date:  2008-06-20       Impact factor: 17.970

9.  NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.

Authors:  Neelaabh Shankar; Tianbing Xia; Scott D Kennedy; Thomas R Krugh; David H Mathews; Douglas H Turner
Journal:  Biochemistry       Date:  2007-10-11       Impact factor: 3.162

10.  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

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  141 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.  The RNA Base-Pairing Problem and Base-Pairing Solutions.

Authors:  Zhipeng Lu; Howard Y Chang
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-12-03       Impact factor: 10.005

3.  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

4.  Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

Authors:  Matthew J Smola; Greggory M Rice; Steven Busan; Nathan A Siegfried; Kevin M Weeks
Journal:  Nat Protoc       Date:  2015-10-01       Impact factor: 13.491

5.  A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class.

Authors:  Marija Košutić; Sandro Neuner; Aiming Ren; Sara Flür; Christoph Wunderlich; Elisabeth Mairhofer; Nikola Vušurović; Jan Seikowski; Kathrin Breuker; Claudia Höbartner; Dinshaw J Patel; Christoph Kreutz; Ronald Micura
Journal:  Angew Chem Int Ed Engl       Date:  2015-10-16       Impact factor: 15.336

6.  Understanding the kinetic mechanism of RNA single base pair formation.

Authors:  Xiaojun Xu; Tao Yu; Shi-Jie Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-22       Impact factor: 11.205

7.  Tuning RNA Flexibility with Helix Length and Junction Sequence.

Authors:  Julie L Sutton; Lois Pollack
Journal:  Biophys J       Date:  2015-12-15       Impact factor: 4.033

8.  RNA conformation: Lightening up invisible states.

Authors:  Yun-Xing Wang
Journal:  Nat Chem Biol       Date:  2016-03       Impact factor: 15.040

Review 9.  Characterizing excited conformational states of RNA by NMR spectroscopy.

Authors:  Bo Zhao; Qi Zhang
Journal:  Curr Opin Struct Biol       Date:  2015-03-10       Impact factor: 6.809

10.  Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Authors:  Konstantin Berlin; Carlos A Castañeda; Dina Schneidman-Duhovny; Andrej Sali; Alfredo Nava-Tudela; David Fushman
Journal:  J Am Chem Soc       Date:  2013-11-06       Impact factor: 15.419

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