Thermodynamic and kinetic aspects of RNA pulling experiments

Biophysical Journal

Volumn 88, Issue 5, 2005, Pages 3224-3242

  Manosas, M ^a   Ritort, Felix ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM ION; POLYMER; RNA;

ARTICLE; EXPERIMENT; FORCE; KINETICS; LASER; MODEL; OPTICS; RNA STRUCTURE; RNA UNFOLDING; TEMPERATURE; THERMODYNAMICS;

EID: 17844397196     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.045344     Document Type: Article

References (38)

1. Bell, I. G. 1978. Models for the specific adhesion of cells to cells. Science. 200:618-627.
2. Bokinsky, G., D. Rueda, V. K. Misra, A. Gordus, M. M. Rhodes, H. P. Babcock, N. G. Walter, and X. Zhuang. 2003. Single-molecule transition-state analysis of RNA folding. Proc. Natl. Acad. Sci. USA. 100:9302-9307.
3. Bolhuis, P. G., C. Dellago, P. L. Geissler, and D. Chandler. 2002. Transition path sampling: throwing ropes over dark mountain passes. Annu. Rev. Phys. Chem. 54:291-318.
4. Bouchiat, C., M. Wang, J. Allemand, T. Strick, S. Block, and V. Croquette. 1999. Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys. J. 76:409-413.
5. Bustamante, C., J. F. Marko, E. D. Siggia, and S. Smith. 1994. Entropic elasticity of λ-phage DNA. Science. 265:1599-1600.
6. Bustamante, C., J. Macosko, and G. Wuite. 2000. Grabbing the cat by the tail: manipulating molecules one by one. Nat. Rev. Mol. Cell Biol. 1:130-136.
7. Cluzel, P., A. Lebrun, C. Heller, R. Lavery, J. L. Viovy, D. Chatenay, and F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794.
8. Cocco, S., R. Monasson, and J. Marko. 2003. Slow nucleic acid unzipping from sequence-defined barriers. Eur. Phys. J. E. 10:153-161.
9. Doudna, J. A., and T. R. Cech. 2002. The chemical repertoire of natural ribozymes. Nature. 418:222-228.
10. Essevaz-Roulet, B., U. Bockelmann, and F. Heslot. 1997. Mechanical separation of the complementary strands of DNA. Proc. Natl. Acad. Sci. USA. 94:11935-11940.
11. Evans, E., and K. Richie. 1997. Dynamic strength of molecular adhesion bonds. Biophys. J. 72:1541-1555.
12. Evans, E., and K. Richie. 1999. Strength of a weak bond connecting flexible polymer chains. Biophys. J. 76:2439-2447.
13. Fang, X. W., P. Thiyagarajan, T. R. Sosnick, and T. Pan. 2002. The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl. Acad. Sci. USA. 99:8518-8523.
14. Fernandez, J. M., S. Chu, and A. F. Oberhauser. 2001. Pulling on hair(pins). Science. 292:653-654.
15. Gerland, U., R. Bundschuh, and T. Hwa. 2001. Force-induced denaturation of RNA. Biophys. J. 81:1324-1332.
16. Gerland, U., R. Bundschuh, and T. Hwa. 2003. Mechanically probing the folding pathway of single RNA molecules. Biophys. J. 84:2831-2840.
17. Harlepp, S., T. Marchal, J. Robert, J.-E. Léger, A. Xayaphoummine, H. Isambert, and D. Chatenay. 2003. Probing complex RNA structures by mechanical force. Eur. Phys. J. E. 12:605-615.
18. Hummer G., and A. Szabo. 2003. Kinetics from nonequilibrium single-molecule pulling experiments. Biophys. J. 85:5-15.
19. Imparato, A., and L. Peliti. 2004. Kinetic barriers in RNA unzipping. Eur. Phys. J. B. 39:357-363.
20. Keller, D., D. Swigon, and C. Bustamante. 2003. Relating single-molecule measurements to thermodynamics. Biophys. J. 84:733-738.
21. Liphardt, D., B. Onoa, S. Smith, I. Tinoco, and C. Bustamante. 2001. Reversible unfolding of single RNA molecules by mechanical force. Science. 292:733-737.
22. Liphardt, J., S. Dumont, S. B. Smith, I. Tinoco, Jr., and C. Bustamante. 2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science. 296:1832-1835.
23. Marinari, E., A. Pagnani, and F. Ricci-Tersenghi. 2002. Zero-temperature properties of RNA secondary structures. Phys. Rev. E. 65:041919.
24. Moore, P. B., and T. A. Steitz. 2002. The involvement of RNA in ribosome function. Nature. 418:229-235.
25. Muñoz, V., P. A. Thompson, J. Hofrichter, and W. A. Eaton. 1997. Folding dynamics and mechanism of β-hairpin formation. Nature. 390:196-199.
26. Onoa, B., D. Dumont, J. Liphardt, S. Smith, I. Tinoco, and C. Bustamante. 2003. Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science. 299:1892-1895.
27. Ritort, F., C. Bustamante, and I. Tinoco. 2002. A two-state kinetic model for the unfolding of single molecules by mechanical force. Proc. Natl. Acad. Sci. USA. 99:13544-13548.
28. Ritort, F. 2003. Work fluctuations, transient violations of the second law and free energy recovery in single molecule experiments. Poincaré Seminar. 2:193-226. Preprint arXiv:cond-mat/0401311.
29. Russell, R., X. W. Zhuang, H. P. Babcock, I. S. Millet, S. Doniach, S. Chu, and D. Herschlag. 2002a. Exploring the folding landscape of a structured RNA. Proc. Natl. Acad. Sci. USA. 99:155-160.
30. Russell, R., I. Millet, M. Tate, L. Kwok, B. Nakatani, S. Gruner, S. Mochrie, V. Pande, S. Doniach, D. Herschlag, and L. Pollak. 2002b. Rapid compaction during RNA folding. Proc. Natl. Acad. Sci. USA. 99:4266-4211.
31. Smith, S., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA molecules using magnetic beads. Science. 258:1122-1126.
32. Smith, S., Y. Cui, and C. Bustamante. 1996. The elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
33. Smith, S., Y. Cui, and C. Bustamante. 2003. Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol. 361:134-162.
34. Tinoco, I, and C. Bustamante. 2002. The effect of force on thermodynamics and kinetics of single molecule reactions. Biophys. Chem. 102:513-533.
35. Zarrinkar, P., and J. Williamson. 1994. Kinetic intermediates in RNA folding. Science. 265:918-923.
36. Zhuang, X. W., T. Ha, H. D. Kim, T. Centner, S. Labeit, and S. Chu. 2000a. Fluorescence quenching: a tool for single-molecule protein-folding study. Proc. Natl. Acad. Sci. USA. 97:14241-14244.
37. Zhuang, X. W., L. E. Bartley, H. P. Babcock, R. Russell, T. J. Ha, D. Herschlag, and S. Chu. 2000b. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
38. Zhuang, X. W., H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473-1476.