Literature DB >> 17438300

Real-time control of the energy landscape by force directs the folding of RNA molecules.

Pan T X Li1, Carlos Bustamante, Ignacio Tinoco.   

Abstract

The rugged folding-energy landscapes of RNAs often display many competing minima. How do RNAs discriminate among competing conformations in their search for the native state? By using optical tweezers, we show that the folding-energy landscape can be manipulated to control the fate of an RNA: individual RNA molecules can be induced into either native or misfolding pathways by modulating the relaxation rate of applied force and even be redirected during the folding process to switch from misfolding to native folding pathways. Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies.

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Year:  2007        PMID: 17438300      PMCID: PMC1855384          DOI: 10.1073/pnas.0702137104

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  37 in total

1.  Reversible unfolding of single RNA molecules by mechanical force.

Authors:  J Liphardt; B Onoa; S B Smith; I Tinoco; C Bustamante
Journal:  Science       Date:  2001-04-27       Impact factor: 47.728

2.  The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics.

Authors:  C P Donahue; R S Yadava; S M Nesbitt; M J Fedor
Journal:  J Mol Biol       Date:  2000-01-21       Impact factor: 5.469

3.  Optical-trap force transducer that operates by direct measurement of light momentum.

Authors:  Steven B Smith; Yujia Cui; Carlos Bustamante
Journal:  Methods Enzymol       Date:  2003       Impact factor: 1.600

4.  A La protein requirement for efficient pre-tRNA folding.

Authors:  Ghadiyaram Chakshusmathi; Sang Do Kim; Douglas A Rubinson; Sandra L Wolin
Journal:  EMBO J       Date:  2003-12-15       Impact factor: 11.598

5.  Mfold web server for nucleic acid folding and hybridization prediction.

Authors:  Michael Zuker
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 6.  Force as a useful variable in reactions: unfolding RNA.

Authors:  Ignacio Tinoco
Journal:  Annu Rev Biophys Biomol Struct       Date:  2004

7.  Force-clamp spectroscopy monitors the folding trajectory of a single protein.

Authors:  Julio M Fernandez; Hongbin Li
Journal:  Science       Date:  2004-03-12       Impact factor: 47.728

8.  Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid.

Authors:  Michael T Woodside; Peter C Anthony; William M Behnke-Parks; Kevan Larizadeh; Daniel Herschlag; Steven M Block
Journal:  Science       Date:  2006-11-10       Impact factor: 47.728

9.  Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme.

Authors:  Bibiana Onoa; Sophie Dumont; Jan Liphardt; Steven B Smith; Ignacio Tinoco; Carlos Bustamante
Journal:  Science       Date:  2003-03-21       Impact factor: 47.728

10.  A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate.

Authors:  Elliot Tan; Timothy J Wilson; Michelle K Nahas; Robert M Clegg; David M J Lilley; Taekjip Ha
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-25       Impact factor: 11.205

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  31 in total

Review 1.  RNA reactions one molecule at a time.

Authors:  Ignacio Tinoco; Gang Chen; Xiaohui Qu
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-04-14       Impact factor: 10.005

Review 2.  Taming free energy landscapes with RNA chaperones.

Authors:  Sarah A Woodson
Journal:  RNA Biol       Date:  2010-11-01       Impact factor: 4.652

3.  Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.

Authors:  Zhenjiang Xu; David H Mathews
Journal:  Bioinformatics       Date:  2010-12-30       Impact factor: 6.937

4.  Understanding the kinetic mechanism of RNA single base pair formation.

Authors:  Xiaojun Xu; Tao Yu; Shi-Jie Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-22       Impact factor: 11.205

5.  Direct single-molecule observation of calcium-dependent misfolding in human neuronal calcium sensor-1.

Authors:  Pétur O Heidarsson; Mohsin M Naqvi; Mariela R Otazo; Alessandro Mossa; Birthe B Kragelund; Ciro Cecconi
Journal:  Proc Natl Acad Sci U S A       Date:  2014-08-25       Impact factor: 11.205

6.  Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA.

Authors:  Gang Chen; Jin-Der Wen; Ignacio Tinoco
Journal:  RNA       Date:  2007-10-24       Impact factor: 4.942

7.  Atomic force microscopy reveals parallel mechanical unfolding pathways of T4 lysozyme: evidence for a kinetic partitioning mechanism.

Authors:  Qing Peng; Hongbin Li
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-06       Impact factor: 11.205

8.  A new computational approach for mechanical folding kinetics of RNA hairpins.

Authors:  Song Cao; Shi-Jie Chen
Journal:  Biophys J       Date:  2009-05-20       Impact factor: 4.033

9.  Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes.

Authors:  Changbong Hyeon; Greg Morrison; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-10       Impact factor: 11.205

10.  DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases.

Authors:  Jens Völker; Horst H Klump; Kenneth J Breslauer
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-17       Impact factor: 11.205

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