Force as a useful variable in reactions: unfolding RNA.

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.

[1]  D. Grier.  A revolution in optical manipulation , 2003, Nature.

[2]  A. Gordus,et al.  Single-molecule transition-state analysis of RNA folding , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Michael D. Stone,et al.  Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Tao Pan,et al.  RNA folding: models and perspectives. , 2003, Current opinion in structural biology.

[5]  I. Prigogine.  Chemical Kinetics and Dynamics , 2003, Annals of the New York Academy of Sciences.

[6]  Ignacio Tinoco,et al.  Identifying Kinetic Barriers to Mechanical Unfolding of the T. thermophila Ribozyme , 2003, Science.

[7]  Polly M Fordyce,et al.  Combined optical trapping and single-molecule fluorescence , 2003, Journal of biology.

[8]  C. Bustamante,et al.  Ten years of tension: single-molecule DNA mechanics , 2003, Nature.

[9]  T. Hwa,et al.  Mechanically probing the folding pathway of single RNA molecules. , 2002, Biophysical journal.

[10]  R. Monasson,et al.  Slow nucleic acid unzipping kinetics from sequence-defined barriers , 2002, The European physical journal. E, Soft matter.

[11]  Ignacio Tinoco,et al.  The effect of force on thermodynamics and kinetics of single molecule reactions. , 2002, Biophysical chemistry.

[12]  F. Ritort,et al.  A two-state kinetic model for the unfolding of single molecules by mechanical force , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Nancy R. Forde,et al.  Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Debra J Searles,et al.  Experimental demonstration of violations of the second law of thermodynamics for small systems and short time scales. , 2002, Physical review letters.

[15]  I. Tinoco,et al.  Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality , 2002, Science.

[16]  Sebastian Doniach,et al.  Rapid compaction during RNA folding , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[17]  R. Monasson,et al.  Force and kinetic barriers to initiation of DNA unzipping. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[18]  A. Oberhauser,et al.  Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  U. Bockelmann,et al.  Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. , 2002, Biophysical journal.

[20]  Shi-Jie Chen,et al.  RNA hairpin-folding kinetics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[21]  A. Ansari,et al.  Misfolded loops decrease the effective rate of DNA hairpin formation. , 2002, Physical review letters.

[22]  Ioulia Rouzina,et al.  Thermodynamics of DNA interactions from single molecule stretching experiments. , 2002, Accounts of chemical research.

[23]  X. Zhuang,et al.  Exploring the folding landscape of a structured RNA , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Carlos Bustamante,et al.  Supplemental data for : The Bacteriophage ø 29 Portal Motor can Package DNA Against a Large Internal Force , 2001 .

[25]  G. Charvin,et al.  The manipulation of single biomolecules , 2001 .

[26]  Simona Cocco,et al.  Force and kinetic barriers to unzipping of the DNA double helix , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Yiqing Shen,et al.  Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. K. Treiber,et al.  Beyond kinetic traps in RNA folding. , 2001, Current opinion in structural biology.

[29]  J. Liphardt,et al.  Reversible Unfolding of Single RNA Molecules by Mechanical Force , 2001, Science.

[30]  G. Hummer,et al.  Free energy reconstruction from nonequilibrium single-molecule pulling experiments , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  S. Smith,et al.  Mechanical fatigue in repetitively stretched single molecules of titin. , 2001, Biophysical journal.

[32]  T Hwa,et al.  Force-induced denaturation of RNA. , 2001, Biophysical journal.

[33]  P K Hansma,et al.  Stepwise unfolding of titin under force-clamp atomic force microscopy. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  E. Evans.  Probing the relation between force--lifetime--and chemistry in single molecular bonds. , 2001, Annual review of biophysics and biomolecular structure.

[35]  D. Thirumalai,et al.  Early events in RNA folding. , 2001, Annual review of physical chemistry.

[36]  V. Croquette,et al.  Replication by a single DNA polymerase of a stretched single-stranded DNA. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Janshoff,et al.  Force Spectroscopy of Molecular Systems-Single Molecule Spectroscopy of Polymers and Biomolecules. , 2000, Angewandte Chemie.

[38]  A. Oberhauser,et al.  Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. , 2000, Progress in biophysics and molecular biology.

[39]  X. Zhuang,et al.  A single-molecule study of RNA catalysis and folding. , 2000, Science.

[40]  F. Eckstein,et al.  Dynamics of the RNA hairpin GNRA tetraloop. , 2000, Biochemistry.

[41]  D. Turner,et al.  10 The Interactions That Shape RNA Structure , 1999 .

[42]  Michelle D. Wang,et al.  Estimating the persistence length of a worm-like chain molecule from force-extension measurements. , 1999, Biophysical journal.

[43]  Michelle D. Wang,et al.  Force and velocity measured for single molecules of RNA polymerase. , 1998, Science.

[44]  A Libchaber,et al.  Kinetics of conformational fluctuations in DNA hairpin-loops. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[45]  M R Chance,et al.  RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. , 1998, Science.

[46]  M Chance,et al.  Following the folding of RNA with time-resolved synchrotron X-ray footprinting. , 1998, Methods in enzymology.

[47]  E. Evans,et al.  Dynamic strength of molecular adhesion bonds. , 1997, Biophysical journal.

[48]  C. Jarzynski.  Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[49]  R. Batey,et al.  Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: I. Defining the minimal RNA site. , 1996, Journal of molecular biology.

[50]  H Schindler,et al.  Detection and localization of individual antibody-antigen recognition events by atomic force microscopy. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[51]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[52]  H. Gaub,et al.  Adhesion forces between individual ligand-receptor pairs. , 1994, Science.

[53]  F. Marchesoni,et al.  An analysis of intermediate transverse momentum pion and photon production inpp collisions through a QCD resummation mechanism , 1981 .

[54]  D. Porschke,et al.  Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix. , 1974, Biophysical chemistry.

[55]  D Pörschke,et al.  Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction. , 1974, Biophysical chemistry.

[56]  D. Crothers,et al.  Thermodynamic and kinetic properties of short RNA helices: the oligomer sequence AnGCUn. , 1974, Nucleic acids research.

[57]  D. Poerschke,et al.  A direct measurement of the unzippering rate of a nucleic acid double helix. , 1974, Biophysical chemistry.

[58]  D M Crothers,et al.  Relaxation kinetics of dimer formation by self complementary oligonucleotides. , 1971, Journal of molecular biology.

[59]  P. Doty,et al.  Self-complementary oligoribonucleotides: effects of helix defects and guanylic acid-cytidylic acid base pairs. , 1971, Journal of molecular biology.