Literature DB >> 18555681

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs.

Vincent B Chu1, Daniel Herschlag.   

Abstract

The rapid development of our understanding of the diverse biological roles fulfilled by non-coding RNA has motivated interest in the basic macromolecular behavior, structure, and function of RNA. We focus on two areas in the behavior of complex RNAs. First, we present advances in the understanding of how RNA folding is accomplished in vivo by presenting a mechanism for the action of DEAD-box proteins. Members of this family are intimately associated with almost all cellular processes involving RNA, mediating RNA structural rearrangements and chaperoning their folding. Next, we focus on advances in understanding, and characterizing the basic biophysical forces that govern the folding of complex RNAs. Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.

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Year:  2008        PMID: 18555681      PMCID: PMC2574980          DOI: 10.1016/j.sbi.2008.05.002

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


  126 in total

1.  The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis.

Authors:  M A Engelhardt; E A Doherty; D S Knitt; J A Doudna; D Herschlag
Journal:  Biochemistry       Date:  2000-03-14       Impact factor: 3.162

2.  A single-molecule study of RNA catalysis and folding.

Authors:  X Zhuang; L E Bartley; H P Babcock; R Russell; T Ha; D Herschlag; S Chu
Journal:  Science       Date:  2000-06-16       Impact factor: 47.728

3.  A collapsed non-native RNA folding state.

Authors:  K L Buchmueller; A E Webb; D A Richardson; K M Weeks
Journal:  Nat Struct Biol       Date:  2000-05

4.  Visualizing the splicing of single pre-mRNA molecules in whole cell extract.

Authors:  Daniel J Crawford; Aaron A Hoskins; Larry J Friedman; Jeff Gelles; Melissa J Moore
Journal:  RNA       Date:  2007-11-19       Impact factor: 4.942

5.  Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids.

Authors:  Yu Bai; Max Greenfeld; Kevin J Travers; Vincent B Chu; Jan Lipfert; Sebastian Doniach; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2007-11-09       Impact factor: 15.419

6.  Synthetic antibodies for specific recognition and crystallization of structured RNA.

Authors:  Jing-Dong Ye; Valentina Tereshko; John K Frederiksen; Akiko Koide; Frederic A Fellouse; Sachdev S Sidhu; Shohei Koide; Anthony A Kossiakoff; Joseph A Piccirilli
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-27       Impact factor: 11.205

7.  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

8.  RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.

Authors:  Eckart Bindewald; Robert Hayes; Yaroslava G Yingling; Wojciech Kasprzak; Bruce A Shapiro
Journal:  Nucleic Acids Res       Date:  2007-10-18       Impact factor: 16.971

9.  Measurement of the effect of monovalent cations on RNA hairpin stability.

Authors:  Jeffrey Vieregg; Wei Cheng; Carlos Bustamante; Ignacio Tinoco
Journal:  J Am Chem Soc       Date:  2007-11-13       Impact factor: 15.419

10.  High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis.

Authors:  Somdeb Mitra; Inna V Shcherbakova; Russ B Altman; Michael Brenowitz; Alain Laederach
Journal:  Nucleic Acids Res       Date:  2008-05-13       Impact factor: 16.971

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  29 in total

1.  Predicting ion binding properties for RNA tertiary structures.

Authors:  Zhi-Jie Tan; Shi-Jie Chen
Journal:  Biophys J       Date:  2010-09-08       Impact factor: 4.033

2.  Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.

Authors:  Jan Lipfert; Gary M Skinner; Johannes M Keegstra; Toivo Hensgens; Tessa Jager; David Dulin; Mariana Köber; Zhongbo Yu; Serge P Donkers; Fang-Chieh Chou; Rhiju Das; Nynke H Dekker
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-13       Impact factor: 11.205

3.  Predicting structures and stabilities for H-type pseudoknots with interhelix loops.

Authors:  Song Cao; Shi-Jie Chen
Journal:  RNA       Date:  2009-02-23       Impact factor: 4.942

Review 4.  Importance of diffuse metal ion binding to RNA.

Authors:  Zhi-Jie Tan; Shi-Jie Chen
Journal:  Met Ions Life Sci       Date:  2011

5.  Mrd1p is required for release of base-paired U3 snoRNA within the preribosomal complex.

Authors:  Pär Lundkvist; Sara Jupiter; Asa Segerstolpe; Yvonne N Osheim; Ann L Beyer; Lars Wieslander
Journal:  Mol Cell Biol       Date:  2009-08-24       Impact factor: 4.272

6.  Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

Authors:  Vincent B Chu; Jan Lipfert; Yu Bai; Vijay S Pande; Sebastian Doniach; Daniel Herschlag
Journal:  RNA       Date:  2009-10-22       Impact factor: 4.942

7.  Clustering to identify RNA conformations constrained by secondary structure.

Authors:  Adelene Y L Sim; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-11       Impact factor: 11.205

8.  The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme.

Authors:  Edith M Osborne; W Luke Ward; Max Z Ruehle; Victoria J DeRose
Journal:  Biochemistry       Date:  2009-11-10       Impact factor: 3.162

9.  Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns.

Authors:  Chunxia Chen; Somdeb Mitra; Magdalena Jonikas; Joshua Martin; Michael Brenowitz; Alain Laederach
Journal:  Biophys J       Date:  2013-03-19       Impact factor: 4.033

Review 10.  RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs.

Authors:  Anne E Simon; Lee Gehrke
Journal:  Biochim Biophys Acta       Date:  2009-06-06
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