Literature DB >> 15139818

Force as a useful variable in reactions: unfolding RNA.

Ignacio Tinoco1.   

Abstract

The effect of force on the thermodynamics and kinetics of reactions is described. The key parameters are the difference in end-to-end distance between reactant and product for thermodynamics, and the distance to the transition state for kinetics. I focus the review on experimental results on force unfolding of RNA. Methods to measure Gibbs free energies and kinetics for reversible and irreversible reactions are described. The use of the worm-like-chain model to calculate the effects of force on thermodynamics and kinetics is illustrated with simple models. The main purpose of the review is to describe the simple experiments that have been done so far, and to encourage more people to enter a field that is new and full of opportunities.

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Year:  2004        PMID: 15139818      PMCID: PMC4183144          DOI: 10.1146/annurev.biophys.33.110502.140418

Source DB:  PubMed          Journal:  Annu Rev Biophys Biomol Struct        ISSN: 1056-8700


  54 in total

1.  Force and kinetic barriers to unzipping of the DNA double helix.

Authors:  S Cocco; R Monasson; J F Marko
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-10       Impact factor: 11.205

2.  Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM.

Authors:  Piotr E Marszalek; Hongbin Li; Andres F Oberhauser; Julio M Fernandez
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-26       Impact factor: 11.205

3.  Misfolded loops decrease the effective rate of DNA hairpin formation.

Authors:  A Ansari; Y Shen; S V Kuznetsov
Journal:  Phys Rev Lett       Date:  2002-01-25       Impact factor: 9.161

Review 4.  Beyond kinetic traps in RNA folding.

Authors:  D K Treiber; J R Williamson
Journal:  Curr Opin Struct Biol       Date:  2001-06       Impact factor: 6.809

5.  Force and kinetic barriers to initiation of DNA unzipping.

Authors:  Simona Cocco; Rémi Monasson; John F Marko
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-03-28

6.  Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality.

Authors:  Jan Liphardt; Sophie Dumont; Steven B Smith; Ignacio Tinoco; Carlos Bustamante
Journal:  Science       Date:  2002-06-07       Impact factor: 47.728

Review 7.  A revolution in optical manipulation.

Authors:  David G Grier
Journal:  Nature       Date:  2003-08-14       Impact factor: 49.962

8.  Relaxation kinetics of dimer formation by self complementary oligonucleotides.

Authors:  M E Craig; D M Crothers; P Doty
Journal:  J Mol Biol       Date:  1971-12-14       Impact factor: 5.469

9.  Stepwise unfolding of titin under force-clamp atomic force microscopy.

Authors:  A F Oberhauser; P K Hansma; M Carrion-Vazquez; J M Fernandez
Journal:  Proc Natl Acad Sci U S A       Date:  2001-01-09       Impact factor: 11.205

10.  Combined optical trapping and single-molecule fluorescence.

Authors:  Matthew J Lang; Polly M Fordyce; Steven M Block
Journal:  J Biol       Date:  2003-02-24
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  27 in total

1.  Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods.

Authors:  Pan T X Li; Delphine Collin; Steven B Smith; Carlos Bustamante; Ignacio Tinoco
Journal:  Biophys J       Date:  2005-10-07       Impact factor: 4.033

2.  Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions.

Authors:  Mai Suan Li; Chin-Kun Hu; Dmitri K Klimov; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2005-12-22       Impact factor: 11.205

3.  Folding thermodynamics of pseudoknotted chain conformations.

Authors:  Zoia Kopeikin; Shi-Jie Chen
Journal:  J Chem Phys       Date:  2006-04-21       Impact factor: 3.488

4.  Unusual mechanical stability of a minimal RNA kissing complex.

Authors:  Pan T X Li; Carlos Bustamante; Ignacio Tinoco
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-16       Impact factor: 11.205

Review 5.  Determination of thermodynamics and kinetics of RNA reactions by force.

Authors:  Ignacio Tinoco; Pan T X Li; Carlos Bustamante
Journal:  Q Rev Biophys       Date:  2006-10-16       Impact factor: 5.318

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

Authors:  Pan T X Li; Carlos Bustamante; Ignacio Tinoco
Journal:  Proc Natl Acad Sci U S A       Date:  2007-04-16       Impact factor: 11.205

7.  Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting.

Authors:  Thomas M Hansen; S Nader S Reihani; Lene B Oddershede; Michael A Sørensen
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-27       Impact factor: 11.205

8.  Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results.

Authors:  Jin-Der Wen; Maria Manosas; Pan T X Li; Steven B Smith; Carlos Bustamante; Felix Ritort; Ignacio Tinoco
Journal:  Biophys J       Date:  2007-02-09       Impact factor: 4.033

9.  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

10.  Forced-unfolding and force-quench refolding of RNA hairpins.

Authors:  Changbong Hyeon; D Thirumalai
Journal:  Biophys J       Date:  2006-02-10       Impact factor: 4.033

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