Literature DB >> 28510027

Single-molecule Förster resonance energy transfer studies of RNA structure, dynamics and function.

Mark Helm1,2, Andrei Yu Kobitski3, G Ulrich Nienhaus3,4.   

Abstract

Single-molecule fluorescence microscopy experiments on RNA molecules brought to light the highly complex dynamics of key biological processes, including RNA folding, catalysis of ribozymes, ligand sensing of riboswitches and aptamers, and protein synthesis in the ribosome. By using highly advanced biophysical spectroscopy techniques in combination with sophisticated biochemical synthesis approaches, molecular dynamics of individual RNA molecules can be observed in real time and under physiological conditions in unprecedented detail that cannot be achieved with bulk experiments. Here, we review recent advances in RNA folding and functional studies of RNA and RNA-protein complexes addressed by using single-molecule Förster (fluorescence) resonance energy transfer (smFRET) technique.

Keywords:  RNA; RNA folding; RNA-protein complexes; Single-molecule Förster resonance energy transfer technique

Year:  2009        PMID: 28510027      PMCID: PMC5418384          DOI: 10.1007/s12551-009-0018-3

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  130 in total

Review 1.  Single-molecule folding.

Authors:  Xiaowei Zhuang; Matthias Rief
Journal:  Curr Opin Struct Biol       Date:  2003-02       Impact factor: 6.809

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

Review 3.  RNA and protein folding: common themes and variations.

Authors:  D Thirumalai; Changbong Hyeon
Journal:  Biochemistry       Date:  2005-04-05       Impact factor: 3.162

4.  Probability distribution analysis of single-molecule fluorescence anisotropy and resonance energy transfer.

Authors:  Stanislav Kalinin; Suren Felekyan; Matthew Antonik; Claus A M Seidel
Journal:  J Phys Chem B       Date:  2007-08-03       Impact factor: 2.991

5.  Essential role of an active-site guanine in glmS ribozyme catalysis.

Authors:  Daniel J Klein; Michael D Been; Adrian R Ferré-D'Amaré
Journal:  J Am Chem Soc       Date:  2007-11-09       Impact factor: 15.419

6.  Thiostrepton inhibition of tRNA delivery to the ribosome.

Authors:  Ruben L Gonzalez; Steven Chu; Joseph D Puglisi
Journal:  RNA       Date:  2007-10-19       Impact factor: 4.942

7.  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

8.  Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids.

Authors:  Asif Iqbal; Sinan Arslan; Burak Okumus; Timothy J Wilson; Gerard Giraud; David G Norman; Taekjip Ha; David M J Lilley
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-01       Impact factor: 11.205

9.  Riboswitches in eubacteria sense the second messenger cyclic di-GMP.

Authors:  N Sudarsan; E R Lee; Z Weinberg; R H Moy; J N Kim; K H Link; R R Breaker
Journal:  Science       Date:  2008-07-18       Impact factor: 47.728

10.  A rugged free energy landscape separates multiple functional RNA folds throughout denaturation.

Authors:  Mark A Ditzler; David Rueda; Jingjie Mo; Kristina Håkansson; Nils G Walter
Journal:  Nucleic Acids Res       Date:  2008-11-06       Impact factor: 16.971

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  5 in total

Review 1.  Super-resolution localization microscopy with photoactivatable fluorescent marker proteins.

Authors:  Per Niklas Hedde; G Ulrich Nienhaus
Journal:  Protoplasma       Date:  2013-10-27       Impact factor: 3.356

Review 2.  Recent advances in RNA structurome.

Authors:  Bingbing Xu; Yanda Zhu; Changchang Cao; Hao Chen; Qiongli Jin; Guangnan Li; Junfeng Ma; Siwy Ling Yang; Jieyu Zhao; Jianghui Zhu; Yiliang Ding; Xianyang Fang; Yongfeng Jin; Chun Kit Kwok; Aiming Ren; Yue Wan; Zhiye Wang; Yuanchao Xue; Huakun Zhang; Qiangfeng Cliff Zhang; Yu Zhou
Journal:  Sci China Life Sci       Date:  2022-06-14       Impact factor: 10.372

Review 3.  Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer.

Authors:  Eitan Lerner; Thorben Cordes; Antonino Ingargiola; Yazan Alhadid; SangYoon Chung; Xavier Michalet; Shimon Weiss
Journal:  Science       Date:  2018-01-19       Impact factor: 47.728

4.  Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs.

Authors:  Xiaolin Niu; Ruirui Sun; Zhifeng Chen; Yirong Yao; Xiaobing Zuo; Chunlai Chen; Xianyang Fang
Journal:  Nat Commun       Date:  2021-11-05       Impact factor: 14.919

Review 5.  Real-Time 3D Single Particle Tracking: Towards Active Feedback Single Molecule Spectroscopy in Live Cells.

Authors:  Shangguo Hou; Courtney Johnson; Kevin Welsher
Journal:  Molecules       Date:  2019-08-02       Impact factor: 4.411

  5 in total

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