DNA force-extension curve under uniaxial stretching

Molecular Simulation

Volumn 36, Issue 3, 2010, Pages 221-228

  Dalir, Hamid ^a,b   Nisisako, Takasi ^a   Yanagida, Yasuko ^a   Hatsuzawa, Takeshi ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b NONE   (Japan)

Author keywords

Base stacking interactions; Double helical DNA structure; Hydrogen bond forces; Mechanical properties; Single molecule manipulation

Indexed keywords

BASE PAIRS; BASE-STACKING; DNA MOLECULES; DOUBLE-HELICAL DNA STRUCTURE; DOUBLE-STRANDED DNA (DS-DNA); ELASTIC BENDING; ELASTIC MODELS; FORCE-EXTENSION CURVES; MECHANICAL RESPONSE; ROBUST MODELS; SEQUENCE-DEPENDENT; SINGLE MOLECULE EXPERIMENTS; SINGLE-MOLECULE; TORSIONAL DEFORMATIONS; TORSIONAL RIGIDITY; TRANSITION DATA; UNIAXIAL STRETCHING; WORM-LIKE CHAIN MODELS;

BENDING (DEFORMATION); DNA; HYDROGEN; HYDROGEN BONDS; MECHANICAL PROPERTIES; MOLECULES;

GENES;

EID: 77649148240     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020903193812     Document Type: Article

References (35)

1. W. Saenger, Principles of Nucleic Acid Structure, Springer-Verlag, New York, 1984.
2. B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J.D. Watson, The Molecular Biology of the Cell, Garland, New York, 1994.
3. J. Widom, Role of DNA sequence in nucleosome stability and dynamics, Q. Rev. Biophys. 34 (2001), pp. 269-324.
4. H. Zhou, Y. Zhang, and Z. Ou-Yang, Elastic property of single double-stranded DNA molecules: Theoretical study and comparison with experiments, Phys. Rev. E 62 (2000), pp. 1045-1058.
5. S.W. Turner, M. Cabodi, and H.G. Craighead, Confinement-induced entropic recoil of single DNA molecules in a nanofluidic structure, Phys. Rev. Lett. 88 (2002), pp. 128103.1-128103.4.
6. C. Gosse and V. Croquette, Magnetic tweezers: Micromanipulation and force measurement at the molecular level, Biophys. J. 82 (2002), pp. 3314-3329.
7. J. Allemand, D. Bensimon, L. Jullien, A. Bensimon, and V. Croquette, pH-dependent specific binding and combing of DNA, Biophys. J. 73 (1997), pp. 2064-2070.
8. O. Bakajin, T. Duke, C. Chou, S. Chan, R. Austin, and E. Cox, Electrohydrodynamic stretching of DNA in confined environments, Phys. Rev. Lett. 80 (1998), pp. 2737-2740.
9. D. Bensimon, A.J. Simon, V. Croquette, and A. Bensimon, Stretching DNA with a receding meniscus: Experiments and models, Phys. Rev. Lett. 74 (1995), pp. 4754-4757.
10. S.B. Smith, L. Finci, and C. Bustamante, Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads, Science 258 (1992), pp. 1122-1126.
11. J.F. Marko and E.D. Siggia, Stretching DNA, Macromolecules 28 (1995), pp. 8759-8770.
12. P.A. Wiggins and P.C. Nelson, Generalized theory of semiflexible polymers, Phys. Rev. E 73 (2006), pp. 031906.1-031906.13.
13. P.A. Wiggins, T.V. Heijden, F.M. Herrero, A. Spakowitz, R. Phillips, J. Widom, C. Dekker, and P.C. Nelson, High flexibility of DNA on short length scales probed by atomic force microscopy, Nature Nanotechnol. 1 (2006), pp. 137-141.
14. S.B. Smith, Y. Cui, and C. Bustamante, Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded dNA molecules, Science 271 (1996), pp. 795-799.
15. J.F. Leger, G. Romano, A. Sarkar, J. Robert, L. Bourdieu, D. Chatenay, and J.F. Marko, Structural transitions of a twisted and stretched DNA molecule, Phys. Rev. Lett. 83 (1999), pp. 1066-1069.
16. C.J. Benham, Onset of writhing in circular elastic polymers, Phys. Rev. A 39 (1989), pp. 2582-2586.
17. A. Sarkar, J.F. Leger, D. Chatenay, and J.F. Marko, Structural transitions in DNA driven by external force and torque, Phys. Rev. E 63 (2001), pp. 051903.1-051903.10.
18. K.N. Chiang, C.A. Yuan, C.N. Han, and C.Y. Chou, Mechanical characteristic of ss-DNA/ds-DNA molecule under external loading, Appl. Phys. Lett. 88 (2006), pp. 023902.1-023902.3.
19. S. Keten and M.J. Buehler, Strength limit of entropic elasticity in beta-sheet protein domains, Phys. Rev. E 78 (2008), pp. 061913.1-061913.7.
20. P.E. Marszalek, H. Lu, H.B. Li, M.C. Vazquez, A.F. Oberhauser, K. Schulten, and J.M. Fernandez, Mechanical unfolding intermediates in titin modules, Nature 402 (1999), pp. 100-103.
21. G.I. Bell, Models for the specific adhesion of cells to cells, Science 200 (1978), pp. 618-627.
22. T. Ackbarow, X. Chen, S. Keten, and M.J. Buehler, Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of α-helical and β-sheet protein domains, Proc. Natl Acad. Sci. USA 104 (2007), pp. 16410-16415.
23. E. Evans and K. Ritchie, Dynamic strength of molecular adhesion bonds, Biophys. J. 72 (1997), pp. 1541-1555.
24. R. Merkel, P. Nassoy, A. Leung, K. Ritchie, and E. Evans, Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy, Nature 397 (1999), pp. 50-53.
25. M. Rief, J.M. Fernandez, and H.E. Gaub, Elastically coupled two-level systems as a model for biopolymer extensibility, Phys. Rev. Lett. 81 (1998), pp. 4764-4767.
26. J.D. Watson, N.H. Hopkins, J.W. Roberts, J.A. Steitz, and A.M. Weiner, Molecular Biology of the Gene, 4th ed., Benjamin/Cummings, Menlo Park, CA, 1987.
27. C. Storm and P.C. Nelson, Theory of high-force DNA stretching and overstretching, Phys. Rev. E 67 (2003), pp. 051906.1-051906.12.
28. G.A. Jeffery and W. Saneger, Hydrogen Bonding in Biological Structures, 1st ed., Springer, Berlin, 1994.
29. A.C. Ansel and S.K. Fenster, Strength and Applied Elasticity, 4th ed., Prentice-Hall, Upper Saddle River, NJ, 2003.
30. S.L. Mayo, B.D. Olafson, and W.A. Goddard, DREIDING: A generic force field for molecular simulations, J. Phys. Chem. 94 (1990), pp. 8897-8909.
31. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M.J. Karplus, CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, Comput. Chem. 4 (1983), pp. 187-217.
32. R.M. Wachter and B.P. Branchaud, Molecular modeling studies on oxidation of hexopyranoses by galactose oxidase. An active site topology apparently designed to catalyze radical reactions, either concerted or stepwise, J. Am. Chem. Soc. 118 (1996), pp. 2782-2789.
33. A. Lebrun and R. Lavery, Modelling extreme stretching of DNA, Nucleic Acids Res. 24 (1996), pp. 2260-2267.
34. M. Wilkins, R. Gosling, and W. Seeds, Physical studies of nucleic acid: Nucleic acid: An extensible molecule? Nature 167 (1951), pp. 759-760.
35. A. Bensimon, A. Simon, A. Chiffaudel, V. Croquette, F. Heslot, and D. Bensimon, Alignment and sensitive detection of DNA by a moving interface, Science 265 (1994), pp. 2096-2098.