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Literature DB >> 20161154

Single-Molecule Fluorescence Studies of RNA: A Decade's Progress.

Krishanthi S Karunatilaka¹, David Rueda.

Abstract

Over the past decade, single-molecule fluorescence studies have elucidated the structure-function relationship of RNA molecules. The real-time observation of individual RNAs by single-molecule fluorescence has unveiled the dynamic behavior of complex RNA systems in unprecedented detail, revealing the presence of transient intermediate states and their kinetic pathways. This review provides an overview of how single-molecule fluorescence has been used to explore the dynamics of RNA folding and catalysis.

Entities: CellLine Chemical Disease Species

Year: 2009 PMID： 20161154 PMCID： PMC2734092 DOI： 10.1016/j.cplett.2009.06.001

Source DB: PubMed Journal: Chem Phys Lett ISSN： 0009-2614 Impact factor: 2.328

93 in total

1. Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Förster distance dependence and subpopulations.

Authors: A A Deniz; M Dahan; J R Grunwell; T Ha; A E Faulhaber; D S Chemla; S Weiss; P G Schultz
Journal: Proc Natl Acad Sci U S A Date: 1999-03-30 Impact factor: 11.205

Review 2. Single-molecule folding.

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

Review 3. Single-molecule fluorescence of nucleic acids.

Authors: Emilia T Mollova
Journal: Curr Opin Chem Biol Date: 2002-12 Impact factor: 8.822

4. 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

5. Experimental observation of optically trapped atoms.

Authors:
Journal: Phys Rev Lett Date: 1986-07-21 Impact factor: 9.161

6. Unusual resistance of peptidyl transferase to protein extraction procedures.

Authors: H F Noller; V Hoffarth; L Zimniak
Journal: Science Date: 1992-06-05 Impact factor: 47.728

Review 7. Exploring RNA folding one molecule at a time.

Authors: Elvin A Alemán; Rajan Lamichhane; David Rueda
Journal: Curr Opin Chem Biol Date: 2008-10-07 Impact factor: 8.822

8. Observation of internal cleavage and ligation reactions of a ribozyme.

Authors: Michelle K Nahas; Timothy J Wilson; Sungchul Hohng; Kaera Jarvie; David M J Lilley; Taekjip Ha
Journal: Nat Struct Mol Biol Date: 2004-10-10 Impact factor: 15.369

Review 9. Modulating the expression of disease genes with RNA-based therapy.

Authors: Matthew Wood; Haifang Yin; Graham McClorey
Journal: PLoS Genet Date: 2007-06 Impact factor: 5.917

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

8 in total

1. Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy.

Authors: Meng Zhao; Fabio D Steffen; Richard Börner; Michelle F Schaffer; Roland K O Sigel; Eva Freisinger
Journal: Nucleic Acids Res Date: 2018-02-16 Impact factor: 16.971

2. TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

Authors: Nicholas J P Wiebe; Irmtraud M Meyer
Journal: PLoS Comput Biol Date: 2010-06-24 Impact factor: 4.475

Single-Molecule Fluorescence Studies of RNA: A Decade's Progress.

1. Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Förster distance dependence and subpopulations.

Review 2. Single-molecule folding.

Review 3. Single-molecule fluorescence of nucleic acids.

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

5. Experimental observation of optically trapped atoms.

6. Unusual resistance of peptidyl transferase to protein extraction procedures.

Review 7. Exploring RNA folding one molecule at a time.

8. Observation of internal cleavage and ligation reactions of a ribozyme.

Review 9. Modulating the expression of disease genes with RNA-based therapy.

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

1. Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy.

2. TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

Review 3. Helicase-mediated changes in RNA structure at the single-molecule level.

4. Regeneration of PEG slide for multiple rounds of single-molecule measurements.

5. Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET.

6. Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle.

7. Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex.

Review 8. Advances in RNA 3D Structure Modeling Using Experimental Data.