DNA stretching modeled at the base pair level: Overtwisting and shear instability in elastic linkages

International Journal of Non-Linear Mechanics

Volumn 47, Issue 6, 2012, Pages 639-654

  Kocsis, Attila ^a   Swigon, David ^b  

^a BUDAPEST UNIVERSITY OF TECHNOLOGY AND ECONOMICS   (Hungary)

^b UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Bifurcations; Discrete elastic model; DNA mechanics; Overstretching; Simplex algorithm

Indexed keywords

BASE PAIRS; BIFURCATION DIAGRAM; DNA MECHANICS; DNA MOLECULES; DNA STRETCHING; ELASTIC ENERGY; ELASTIC LINKAGE; ELASTIC MODELS; ELASTIC RESPONSE; EQUILIBRIUM CONFIGURATION; FORCE-DISPLACEMENT DIAGRAMS; LEVEL MODEL; OVERSTRETCHING; OVERTWISTING; QUADRATIC FORM; QUADRATIC MODELS; SEQUENCE-DEPENDENT; SHEAR INSTABILITY; SIMPLEX ALGORITHM; SINGLE DNA MOLECULES;

BIFURCATION (MATHEMATICS); MOLECULES; NUMBER THEORY; SWITCHING NETWORKS;

DNA;

EID: 84861580135     PISSN: 00207462     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijnonlinmec.2011.10.008     Document Type: Article

References (49)

1. R. Dickerson, M. Bansal, C. Calladine, S. Diekmann, W. Hunter, O. Kennard, E. von Kitzing, R. Lavery, H. Nelson, W. Olson, W. Saenger, H. Sklenar, D. Soumpasis, C.-S. Tung, A.-J. Wang, and V. Zhurkin Definition and nomenclature of nucleic acid structure parameters, the Cambridge accord EMBO Journal 8 1988 1 4
2. T. Thundat, D. Allison, and R. Warmack Stretched DNA structures observed with atomic force microscopy Nucleic Acids Research 22 1994 4224 4228
3. P. Cluzel, A. Lebrun, C. Heller, R. Lavery, J. Viovy, D. Chatenay, and F. Caron DNA: an extensible molecule Science 271 1996 792 794
4. M. Wang, H. Yin, R. Landick, J. Gelles, and S. Block Stretching DNA with optical tweezers Biophysical Journal 72 1997 1335 1346
5. S. Smith, Y. Cui, and C. Bustamante Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 1996 795 799
6. C. Bustamante, S. Smith, J. Liphardt, and D. Smith Single-molecule studies of DNA mechanics Current Opinion in Structural Biology 10 2000 279 285
7. S. Smith, L. Finzi, and C. Bustamante Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads Science 258 1992 1122 1126
8. J. Gore, Z. Bryant, M. Nöllmann, M. Le, N. Cozzarelli, and C. Bustamante DNA overwinds when stretched Nature 442 2006 836 839
9. F. Mosconi, J. Allemand, D. Bensimon, and V. Croquette Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers Physical Review Letters 102 2009 078301 1-4
10. 3 Nano Letters 5 2005 1509 1514
11. C. Danilowicza, C. Limousea, K. Hatcha, A. Conovera, V. Coljeea, N. Klecknerb, and M. Prentissa The structure of DNA overstretched from the 5 ′ 5 ′ ends differs from the structure of DNA overstretched from the 3 ′ 3 ′ ends Proceedings of the National Academy of Sicence USA 106 2009 13196 13201
12. M. Sheinin, and M. Wang Twist-stretch coupling and phase transition during DNA supercoiling Physical Chemistry Chemical Physics 11 2009 4800 4803
13. J. Léger, G. Romano, A. Sarkar, J. Robert, L. Bourdieu, D. Chatenay, and J. Marko Structural transitions of a twisted and stretched DNA molecule Physical Review Letters 83 1999 1066 1069
14. M. Williams, I. Rouzina, and M. McCauley Peeling back the mystery of DNA overstretching Proceedings of the National Academy of Sicence USA 106 2009 18047 18048
15. J. van Mameren, P. Gross, G. Farge, P. Hooijman, M. Modesti, M. Falkenberg, G. Wuite, and E. Peterman Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging Proceedings of the National Academy of Sicence USA 106 2009 18231 18236
16. H. Fu, H. Chen, J. Marko, and J. Yan Two distinct overstretched DNA states Nucleic Acids Research 30 2010 5594 5600
17. S. Cocco, J. Yan, J. Léger, D. Chatenay, and J. Marko Overstretching and force-driven strand separation of double-helix DNA Physical Review E 70 2004 011910 1-18
18. M.L. Bret Catastrophic variation of twist and writhing of circular DNAs with constraint? Biopolymers 18 1979 1709 1725
19. I. Tobias, B. Coleman, and W. Olson The dependence of DNA tertiary structure on end conditions: theory and implications for topological transitions Journal of Chemical Physics 101 1994 10990 10996
20. B. Coleman, and D. Swigon Theory of supercoiled elastic rings with self-contact and its application to DNA plasmids Journal of Elasticity 60 2000 173 221
21. O. Kratky, and G. Porod Rontgenuntersuchung geloster fadenmolekule Recueil des Travaux Chimiques des Pays-Bas 68 1949 1106 1122
22. W. Olson, A. Gorin, X.-J. Lu, L. Hock, and V. Zhurkin DNA sequence-dependent deformability deduced from protein-DNA crystal complexes PNAS Biophysics 95 1998 11163 11168
23. S. Dixit, D. Beveridge, D. Case, T. Cheatham, E. Giudice, F. Lankas, R. Lavery, J. Maddocks, R. Osman, H. Sklenar, K. Thayer, and P. Varnai Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides ii: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps Biophysical Journal 89 2005 3721 3740
24. S. Antman Nonlinear Problems of Elasticity 2005 Springer New York
25. D. Dichmann, Y. Li, and J. Maddocks Hamiltonian formulations and symmetries in rod mechanics Mathematical Approaches to Biomolecular Structure and Dynamics 82 1996 71 113
26. P. Furrer, R. Manning, and J. Maddocks DNA rings with multiple energy minima Biophysical Journal 79 1 2000 116 136
27. H. Weiss Dynamics of geometrically nonlinear rods: I. Mechanical models and equations of motion Nonlinear Dynamics 30 4 2002 357 381
28. O. Gonzalez, and J. Maddocks Extracting parameters for base-pair level models of DNA from molecular dynamics simulations Theoretical Chemistry Accounts 106 2001 76 82
29. B. Coleman, W. Olson, and D. Swigon Theory of sequence-dependent DNA elasticity Journal of Chemical Physics 118 2003 7127 7140
30. N. Becker From rigid base pairs to semiflexible polymers: coarse-graining DNA Physical Review E 76 2007 021923 1-17
31. M.E. Hassan, and C. Calladine The assessment of the geometry of dinucleotide steps in double-helical DNA: a new local calculation scheme Journal of Molecular Biology 251 1995 648 664
32. Z. Gáspár, G. Domokos, and I. Szeberényi A parallel algorithm for the global computation of elastic bar structures CAMES 4 1997 55 68
33. G. Domokos, and Z. Gáspár A global, direct algorithm for path-following and active static control of elastic bar structures Mechanics of Structures and Machines 23 1995 549 571
34. E. Allgower, and K. Georg Numerical Continuation Methods: An Introduction 1990 Springer-Verlag Berlin
35. W. Olson, D. Swigon, and B. Coleman Implications of the dependence of the elastic properties of DNA on nucleotide sequence Philosophical Transactions of the Royal Society of London A 362 2004 1403 1422
36. 〈 http://dnaserver.rutgers.edu/database.php 〉.
37. S. Antman, and E. Carbone Shear and necking instabilities in nonlinear elasticity Journal of Elasticity 7 1977 125 151
38. S. Timoshenko Theory of Elastic Stability 1936 McGraw-Hill London
39. A. Kocsis, R. Németh, and G. Károlyi Spatially chaotic bifurcations of an elastic web of links International Journal of Bifurcation and Chaos 20 2011 4011 4028
40. T. Cloutier, and J. Widom Spontaneous sharp bending of double-stranded DNA Molecular Cell 14 2004 355 362
41. Q. Du, C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. Vologodskii Cyclization of short DNA fragments and bending fluctuations of the double helix Proceedings of the National Academy of Sicence USA 102 2005 5397 5402
42. C. Yuan, H. Chen, X. Lou, and L. Archer DNA bending stiffness on small length scales Physical Review Letters 100 2008 018102 1-4
43. M. Peyrard, and A. Bishop Statistical mechanics of a nonlinear model for DNA denaturation Physical Review Letters 62 23 1989 2755 2758
44. G. Saccomandi, and I. Sgura The relevance of nonlinear stacking interactions in simple models of double-stranded DNA Journal of the Royal Society Interface 3 10 2006 655
45. A. Kocsis, and G. Károlyi Conservative spatial chaos of buckled elastic linkages Chaos 16 2006 03111/1-7
46. G. Domokos, and P. Holmes Eulers problem,eulers method, and the standard map; or, the discrete charm of buckling Journal of Nonlinear Science 3 1993 109 151
47. G. Gaeta On a model of DNA torsion dynamics Physics Letters A 143 4-5 1990 227 232
48. S. Kehrbaum, and J. Maddocks Effective properties of elastic rods with high intrinsic twist Proceedings of the 16th IMACS World Congress vol. 2000 2000
49. 〈 http://www.pittgrid.pitt.edu 〉.