Measuring the folding landscape of a harmonically constrained biopolymer

Biophysical Journal

Volumn 100, Issue 11, 2011, Pages 2736-2744

  De Messieres, Michel ^a   Brawn Cinani, Barbara ^a   La Porta, Arthur ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79960305090     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.03.067     Document Type: Article

References (37)

1. Arrhenius, S. 1889. On the rate of reaction of the inversion of sucrose by acids. Z. Phys. Chem. 4:226-248.
2. Eyring, H. 1935. The activated complex in chemical reactions. J. Chem. Phys. 3:107-115.
3. Laidler, K. J., and M. C. King. 1983. The development of transitionstate theory. J. Phys. Chem. 87:2657-2664.
4. Kramers, H. A. 1940. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica. VII:284-304.
5. Plotkin, S. S., and J. N. Onuchic. 2002. Understanding protein folding with energy landscape theory. Part I: Basic concepts. Q. Rev. Biophys. 35:111-167. (Pubitemid 34875513)
6. Onuchic, J. N., and P. G. Wolynes. 2004. Theory of protein folding. Curr. Opin. Struct. Biol. 14:70-75. (Pubitemid 38249595)
7. Wolynes, P. G., J. N. Onuchic, and D. Thirumalai. 1995. Navigating the folding routes. Science. 267:1619-1620.
8. Dill, K. A., S. B. Ozkan, ., T. R. Weikl. 2008. The protein folding problem. Annu. Rev. Biophys. 37:289-316.
9. Borgia, A., P. M. Williams, and J. Clarke. 2008. Single-molecule studies of protein folding. Annu. Rev. Biochem. 77:101-125.
10. Neuman, K. C., and A. Nagy. 2008. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat. Methods. 5:491-505. (Pubitemid 351761756)
11. Evans, E. 1999. Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy. Biophys. Chem. 82:83-97.
12. Dudko, O. K., G. Hummer, and A. Szabo. 2008. Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc. Natl. Acad. Sci. USA. 105:15755-15760.
13. Evans, E. 2001. Probing the relation between force-lifetime-and chemistry in single molecular bonds. Annu. Rev. Biophys. Biomol. Struct. 30:105-128. (Pubitemid 32566158)
14. Koch, S. J., and M. D. Wang. 2003. Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA. Phys. Rev. Lett. 91:028103.
15. Lynch, S., H. Baker, ..., K. Sinniah. 2009. Single molecule force spectroscopy on G-quadruplex DNA. Chemistry. 15:8113-8116.
16. Liphardt, J., B. Onoa, ...., C. Bustamante. 2001. Reversible unfolding of a single RNA molecule by mechanical force. Science. 292:733-737. (Pubitemid 32385545)
17. Woodside, M. T., P. C. Anthony, ...., S. M. Block. 2006. Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science. 314:1001-1004. (Pubitemid 44749947)
18. Woodside, M. T., W. M. Behnke-Parks, ...., S. M. Block. 2006. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc. Natl. Acad. Sci. USA. 103:6190-6195.
19. Hyeon, C., G. Morrison, and D. Thirumalai. 2008. Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc. Natl. Acad. Sci. USA. 105:9604-9609. (Pubitemid 352031347)
20. Wen, J.-D., M. Manosas, ..., I. Tinoco Jr. 2007. Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys. J. 92:2996-3009. (Pubitemid 46684561)
21. Manosas, M., J.-D. Wen, ...., F. Ritort. 2007. Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Biophys. J. 92:3010-3021. (Pubitemid 46684562)
22. Torrie, G. M., and J. P. Valleau. 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys. 23:187-199.
23. Kumar, S., D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg. 1992. The weighted histogram analysis method for freeenergy calculations on biomolecules. I. The method. J. Comput. Chem. 13:1011-1021.
24. Denesyuk, N. A., and J. D. Weeks. 2009. Equilibrium and nonequilibrium effects in the collapse of a model polypeptide. Phys. Rev. Lett. 102:108101.
25. Greenleaf, W. J., M. T. Woodside, ...., S. M. Block. 2005. Passive alloptical force clamp for high-resolution laser trapping. Phys. Rev. Lett. 95:208102.
26. Shaevitz, J. W., E. A. Abbondanzieri, ...., S. M. Block. 2003. Backtracking by single RNA polymerase molecules observed at nearbase- pair resolution. Nature. 426:684-687. (Pubitemid 38009379)
27. Junier, I., A. Mossa, ...., F. Ritort. 2009. Recovery of free energy branches in single molecule experiments. Phys. Rev. Lett. 102:070602.
28. Huguet, J. M., C. V. Bizarro, ..., F. Ritort. 2010. Single-molecule derivation of salt dependent base-pair free energies in DNA. Proc. Natl. Acad. Sci. USA. 107:15431-15436.
29. Landry, M. P., P. M. McCall, ..., Y. R. Chemla. 2009. Characterization of photoactivated singlet oxygen damage in single-molecule optical trap experiments. Biophys. J. 97:2128-2136.
30. Pralle, A., M. Prummer, ...., J. K. Hörber. 1999. Three-dimensional high-resolution particle tracking for optical tweezers by forward scattered light. Microsc. Res. Tech. 44:378-386. (Pubitemid 29122775)
31. Marko, J. F., and E. D. Siggia. 1995. Stretching DNA. Macromolecules. 28:8759-8770.
32. Saenger, W. 1988. Principles of Nucleic Acid Structure. Springer-Verlag, New York.
33. Wang, M. D., H. Yin, ..., S. M. Block. 1997. Stretching DNA with optical tweezers. Biophys. J. 72:1335-1346. (Pubitemid 27113656)
34. Svoboda, K., and S. M. Block. 1994. Biological applications of optical forces. Annu. Rev. Biophys. Biomol. Struct. 23:247-285. (Pubitemid 24217369)
35. Peyret, N. 2000. Prediction of nucleic acid hybridization: parameters and algorithms. PhD dissertation. Wayne State University, Detroit, MI.
36. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415. (Pubitemid 37442169)
37. SantaLucia Jr., J. J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.