Literature DB >> 17594140

NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.

Melissa Getz1, Xiaoyan Sun, Anette Casiano-Negroni, Qi Zhang, Hashim M Al-Hashimi.   

Abstract

An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipolar couplings (RDCs) in partially aligned systems is providing new insights into the structural plasticity of RNA through combined characterization of large-amplitude collective helix motions and local flexibility in noncanonical regions over a wide window of biologically relevant timescales (<milliseconds). Here, we review RDC methodology for studying RNA structural dynamics and survey what has been learnt thus far from application of these methods. Future methodological challenges are also identified.

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Year:  2007        PMID: 17594140     DOI: 10.1002/bip.20765

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  47 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

2.  Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA.

Authors:  Qi Zhang; Nak-Kyoon Kim; Robert D Peterson; Zhonghua Wang; Juli Feigon
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-21       Impact factor: 11.205

3.  3D maps of RNA interhelical junctions.

Authors:  Maximillian H Bailor; Anthony M Mustoe; Charles L Brooks; Hashim M Al-Hashimi
Journal:  Nat Protoc       Date:  2011-09-15       Impact factor: 13.491

4.  Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media.

Authors:  Michael P Latham; Paul Hanson; Darin J Brown; Arthur Pardi
Journal:  J Biomol NMR       Date:  2007-11-17       Impact factor: 2.835

5.  Solid-state deuterium NMR studies reveal micros-ns motions in the HIV-1 transactivation response RNA recognition site.

Authors:  Greg L Olsen; Dorothy C Echodu; Zahra Shajani; Michael F Bardaro; Gabriele Varani; Gary P Drobny
Journal:  J Am Chem Soc       Date:  2008-02-15       Impact factor: 15.419

6.  Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.

Authors:  James E Johnson; Charles G Hoogstraten
Journal:  J Am Chem Soc       Date:  2008-12-10       Impact factor: 15.419

7.  Dynamics of tRNA at different levels of hydration.

Authors:  J H Roh; R M Briber; A Damjanovic; D Thirumalai; S A Woodson; A P Sokolov
Journal:  Biophys J       Date:  2009-04-08       Impact factor: 4.033

8.  Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

Authors:  Elizabeth A Dethoff; Alexandar L Hansen; Catherine Musselman; Eric D Watt; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

Review 9.  Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs.

Authors:  Vincent B Chu; Daniel Herschlag
Journal:  Curr Opin Struct Biol       Date:  2008-06       Impact factor: 6.809

10.  Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.

Authors:  Maximillian H Bailor; Catherine Musselman; Alexandar L Hansen; Kush Gulati; Dinshaw J Patel; Hashim M Al-Hashimi
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

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