Literature DB >> 21882345

RNA dynamics: perspectives from spin labels.

Phuong Nguyen1, Peter Z Qin.   

Abstract

Dynamics are important and indispensible physical attributes that play essential roles in RNA function. RNA dynamics are complex, spanning vast timescales, and encompassing a large number of physical modes. The technique of site-directed spin labeling (SDSL), which derives information on local structural and dynamic features of a macromolecule by monitoring a chemically stable nitroxide radical using electron paramagnetic resonance spectroscopy, has been applied to monitor intrinsic dynamics at defined structural states as well as to probe conformational transition dynamics of RNAs. The current state of SDSL studies of RNA dynamics is summarized here. Further development and application of SDSL promise to open up many more opportunities for probing RNA dynamics and connecting dynamics to structure and function.
Copyright © 2011 John Wiley & Sons, Ltd.

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Year:  2011        PMID: 21882345      PMCID: PMC3235270          DOI: 10.1002/wrna.104

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev RNA        ISSN: 1757-7004            Impact factor:   9.957


  72 in total

Review 1.  Identifying conformational changes with site-directed spin labeling.

Authors:  W L Hubbell; D S Cafiso; C Altenbach
Journal:  Nat Struct Biol       Date:  2000-09

2.  Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA.

Authors:  Laura E Bartley; Xiaowei Zhuang; Rhiju Das; Steven Chu; Daniel Herschlag
Journal:  J Mol Biol       Date:  2003-05-16       Impact factor: 5.469

3.  Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling.

Authors:  Xiaojun Zhang; Sang Won Lee; Liang Zhao; Tianbing Xia; Peter Z Qin
Journal:  RNA       Date:  2010-10-27       Impact factor: 4.942

4.  EPR methods to study specific metal-ion binding sites in RNA.

Authors:  Laura Hunsicker-Wang; Matthew Vogt; Victoria J Derose
Journal:  Methods Enzymol       Date:  2009-11-17       Impact factor: 1.600

5.  Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR.

Authors:  Dorith Wunnicke; Denise Strohbach; Julia E Weigand; Bettina Appel; Emiliano Feresin; Beatrix Suess; Sabine Müller; Heinz-Jürgen Steinhoff
Journal:  RNA       Date:  2010-11-19       Impact factor: 4.942

6.  The RNA-DNA hybrid structure determined by EPR, CD and RNase H1.

Authors:  Olga Romainczyk; Burkhard Endeward; Thomas F Prisner; Joachim W Engels
Journal:  Mol Biosyst       Date:  2011-02-19

7.  Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy.

Authors:  Ivan Krstić; Robert Hänsel; Olga Romainczyk; Joachim W Engels; Volker Dötsch; Thomas F Prisner
Journal:  Angew Chem Int Ed Engl       Date:  2011-04-19       Impact factor: 15.336

8.  Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B.

Authors:  C Faber; H Sticht; K Schweimer; P Rösch
Journal:  J Biol Chem       Date:  2000-07-07       Impact factor: 5.157

9.  Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy.

Authors:  Xiaojun Zhang; Pavol Cekan; Snorri Th Sigurdsson; Peter Z Qin
Journal:  Methods Enzymol       Date:  2009-11-17       Impact factor: 1.600

10.  Mapping global folds of oligonucleotides by pulsed electron-electron double resonance.

Authors:  Olav Schiemann
Journal:  Methods Enzymol       Date:  2009-11-17       Impact factor: 1.600

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  19 in total

1.  Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.

Authors:  Leah M Seebald; Christopher M DeMott; Srivathsan Ranganathan; Papa Nii Asare-Okai; Anastasia Glazunova; Alan Chen; Alexander Shekhtman; Maksim Royzen
Journal:  J Inorg Biochem       Date:  2017-02-24       Impact factor: 4.155

2.  Continuous wave W- and D-band EPR spectroscopy offer "sweet-spots" for characterizing conformational changes and dynamics in intrinsically disordered proteins.

Authors:  Thomas M Casey; Zhanglong Liu; Jackie M Esquiaqui; Natasha L Pirman; Eugene Milshteyn; Gail E Fanucci
Journal:  Biochem Biophys Res Commun       Date:  2014-06-17       Impact factor: 3.575

3.  Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA.

Authors:  Yan Sun; Peter P Borbat; Vladimir M Grigoryants; William K Myers; Jack H Freed; Charles P Scholes
Journal:  Biophys J       Date:  2015-02-17       Impact factor: 4.033

4.  A Straightforward Approach to the Analysis of Double Electron-Electron Resonance Data.

Authors:  Richard A Stein; Albert H Beth; Eric J Hustedt
Journal:  Methods Enzymol       Date:  2015-09-15       Impact factor: 1.600

5.  From a structural average to the conformational ensemble of a DNA bulge.

Authors:  Xuesong Shi; Kyle A Beauchamp; Pehr B Harbury; Daniel Herschlag
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-31       Impact factor: 11.205

6.  Synthesis of DNA and RNA Oligonucleotides Containing a Dual-Purpose Selenium-Modified Fluorescent Nucleoside Probe.

Authors:  Ashok Nuthanakanti; Seergazhi G Srivatsan
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2020-06

7.  A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme.

Authors:  Phuong Nguyen; Xuesong Shi; Snorri Th Sigurdsson; Daniel Herschlag; Peter Z Qin
Journal:  Chembiochem       Date:  2013-07-30       Impact factor: 3.164

8.  Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling.

Authors:  Xiaojun Zhang; Chang-Shung Tung; Glenna Z Sowa; Ma'mon M Hatmal; Ian S Haworth; Peter Z Qin
Journal:  J Am Chem Soc       Date:  2012-01-27       Impact factor: 15.419

9.  Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.

Authors:  Anna M Popova; Ma'mon M Hatmal; Maria P Frushicheva; Eric A Price; Peter Z Qin; Ian S Haworth
Journal:  J Phys Chem B       Date:  2012-05-23       Impact factor: 2.991

10.  A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.

Authors:  Phuong H Nguyen; Anna M Popova; Kálmán Hideg; Peter Z Qin
Journal:  BMC Biophys       Date:  2015-04-09       Impact factor: 4.778

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