Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

Nature

Volumn 437, Issue 7056, 2005, Pages 231-234

  Collin, D ^a   Ritort, F ^b   Jarzynski, C ^c   Smith, S B ^d   Tinoco Jr , I ^d   Bustamante, C ^d  

^a MERCK RESEARCH LABORATORIES   (United States)

^b UNIVERSITY OF BARCELONA   (Spain)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC FORCE MICROSCOPY; FORCE MEASUREMENT; FREE ENERGY; HYSTERESIS; INFORMATION ANALYSIS; THERMODYNAMIC STABILITY; TRAJECTORIES;

CROOKS FLUCTUATION THEOREM; EQUILIBRIUM INFORMATION; HYSTERESIS EFFECTS; MOLECULAR INTERACTION; OPTICAL TWEEZERS; RNA MOLECULES; THERMODYNAMIC FREE-ENERGY;

RNA;

MAGNESIUM ION; RNA; MAGNESIUM;

BIOLOGY;

ARTICLE; ATOMIC FORCE MICROSCOPY; DISSOCIATION; ENERGY; HYSTERESIS; MATHEMATICAL MODEL; PHASE TRANSITION; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; RNA STRUCTURE; STRUCTURE ANALYSIS; THERMODYNAMICS; BASE PAIRING; CHEMICAL MODEL; CHEMISTRY; CONFORMATION; DRUG EFFECT; GENETICS; METABOLISM; PROBABILITY; REPRODUCIBILITY; RNA STABILITY; STATISTICAL DISTRIBUTION;

BASE PAIRING; MAGNESIUM; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; PROBABILITY; REPRODUCIBILITY OF RESULTS; RNA; RNA STABILITY; STATISTICAL DISTRIBUTIONS; THERMODYNAMICS;

EID: 24644450199     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature04061     Document Type: Article

References (30)

1. Evans, D. J., Cohen, E. G. & Morriss, G. P. Probability of second law violations in shearing steady states. Phys. Rev. Lett. 71, 2401-2404 (1993).
2. Gallavotti, G. & Cohen, E. G. D. Dynamical ensembles in nonequilibrium statistical mechanics. Phys. Rev. Lett. 74, 2694-2697 (1995).
3. Ciliberto, S. & Laroche, C. An experimental test of the Gallavotti-Cohen fluctuation theorem. J. Phys. IV 8(Proc. 6), 215-220 (1998).
4. Evans, D. J. & Searles, D. J. The fluctuation theorem. Adv. Phys. 51, 1529-1585 (2002).
5. Wang, G. M., Sevick, E. M., Mittag, E., Searles, D. J. & Evans, D. J. Experimental demonstration of violations of the second law of thermodynamics for small systems and short timescales. Phys. Rev. Lett. 89, 050601 (2002).
6. Hummer, G. & Szabo, A. Free-energy reconstruction from nonequilibrium single molecule experiments. Proc. Natl Acad Sci. USA 98, 3658-3661 (2001).
7. Liphardt, J., Dumont, S., Smith, S. B., Tinoco, I. Jr & Bustamante, C. Equilibrium information from nonequilibrium measurements in an experimental test of the Jarzynski equality. Science 296, 1832-1835 (2002).
8. Ritort, F., Bustamante, C. & Tinoco, I. Jr A two-state kinetic model for the unfolding of single molecules by mechanical force. Proc. Natl Acad. Sci. USA 99, 13544-13548 (2002).
9. Crooks, G. E. Entropy production fluctuation theorem and the nonequilibrium work relation for free-energy differences. Phys. Rev. E 60, 2721-2726 (1999).
10. Smith, S. B., Cui, Y. & Bustamante, C. An optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol. 361, 134-162 (2003).
11. McManus, M. T., Petersen, C. P., Haines, B. B., Chen, J. & Sharp, A. P. Gene silencing using micro-RNA designed hairpins. RNA 8, 842-850 (2002).
12. Serganov, A. et al. Role of conserved nucleotides in building the 16S rRNA binding site for ribosomal protein S15. J. Mol. Biol. 305, 785-803 (2002).
13. Ritort, F. Work fluctuations, transient violations of the second law and free-energy recovery methods. Semin. Poincaré 2, 193-226 (2003).
14. Jarzynski, C. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78, 2690-2693 (1997).
15. Park, S. & Schulten, K. Calculating potentials of mean force from steered molecular dynamics simulations. J. Chem. Phys. 120, 5946-5961 (2004).
16. Liphardt, J., Onoa, B., Smith, S. B., Tinoco, I. Jr & Bustamante, C. Reversible unfolding of single RNA molecules by mechanical force. Science 292, 733-737 (2001).
17. Zuckerman, D. M. & Woolf, T. B. Theory of systematic computational error in free energy differences. Phys. Rev. Lett. 89, 180602 (2002).
18. Gore, J., Ritort, F. & Bustamante, C. Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proc Natl Acad. Sci. USA 100, 12564-12569 (2003).
19. Shirts, R., Bair, E., Hooker, G. & Pande, V. S. Equilibrium free energies from nonequilibrium measurements using maximum likelihood methods. Phys. Rev. Lett. 91, 140601 (2003).
20. Bennett, C. H. Efficient estimates of free energy differences from Monte Carlo data. J. Comp. Phys. 22, 245-268 (1976).
21. SantaLucia, J. Jr & Hicks, D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415-440 (2004).
22. Robertus, D. J. et al. Structure of yeast phenylalanine tRNA at 3A resolution. Nature 250, 546-551 (1974).
23. Long, D. M. & Uhlenbeck, O. C. Self-cleaving catalytic RNA. FASEB J. 7, 25-30 (1993).
24. Cate, J. H. & Doudna, J. A. Metal binding sites in the major groove of a large ribozyme domain. Structure 4, 1221-1229 (1996).
25. Zuker, M. Mfold web server for nucleic acid folding and hybridization predictions. Nucleic Acids Res. 31, 3406-3415 (2003).
26. Turner, D. H. in Nucleic Acids: Structures, Properties and Functions (eds Bloomfield, D. A., Crothers, D. M. & Tinoco, I. Jr) Ch. 7 (Univ. Press, New York, 2000).
27. Carrion-Vazquez, M., et al. Protein nanomechanics studied by AFM single-molecule force spectroscopy. In Emerging Techniques in Biophysics (eds Arrondo, J. L. R. & Alonso, A.) (Biophys. Monogr. Ser., Springer, Heidelberg, in the press).
28. Milligan, J. F., Groebe, D. R., Withered, G. W. & Uhlenbeck, O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798 (1987).
29. Manosas, M. & Ritort, F. Thermodynarnic and kinetic aspects of RNA pulling experiments. Biophys. J. 88, 3224-3242 (2005).
30. Hummer, G. Fast-growth thermodynamics integration: Error and efficiency analysis. J. Chem. Phys. 114, 7330-7337 (2001).