The dependence of DNA supercoiling on solution electrostatics

Acta Biomaterialia

Volumn 8, Issue 6, 2012, Pages 2133-2143

  Argudo, David ^a   Purohit, Prashant K ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Biological material; DNA plectonemes; Electrostatics; Multivalent counterions; Thermal fluctuations

Indexed keywords

DISSOCIATION; ELECTROSTATICS; ENTROPY; FREE ENERGY;

DNA ELASTICITY; DNA MOLECULES; DNA PLECTONEME; DNA SUPERCOILING; ENTROPIC INTERACTIONS; ISOTROPIC RODS; MULTIVALENT COUNTERIONS; PLECTONEMES; ROD MODEL; THERMAL FLUCTUATIONS;

DNA;

ARTICLE; DNA SUPERCOILING; ELASTICITY; ENTROPY; FORCE; MOTION; PRIORITY JOURNAL; STATIC ELECTRICITY; TORQUE;

EID: 84860541753     PISSN: 17427061     EISSN: 18787568     Source Type: Journal    
DOI: 10.1016/j.actbio.2012.01.030     Document Type: Article

References (62)

1. P. Nelson Biological physics 2004 W.H. Freeman and Company New York
2. D. Koster, V. Croquette, C. Dekker, S. Shuman, and N. Dekker Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB Nature 434 2005 671 674
3. D. Koster, A. Crut, S. Shuman, M. Bjornsti, and N. Dekker Cellular strategies for regulating DNA supercoiling: a single-molecule perspective Cell 142 4 2010 519 530
4. S. Forth, C. Deufel, M.Y. Sheinin, B. Daniels, J.P. Sethna, and D. Wang Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules Phys Rev Lett 100 14 2008 148301
5. Lipfert J, Kerssenmakers J, Jager T, Dekker N. Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments. Nat Methods 2010;Published online doi:10.1038/nmeth.1520, [17 October 2010].
6. F. Mosconi, J. Allemand, D. Bensimon, and V. Croquette Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers Phys Rev Lett 102 7 2009 078301
7. T. Strick, J. Allemand, D. Bensimon, A. Bensimon, and V. Croquette The elasticity of a single supercoiled DNA molecule Science 271 5257 1996 1835 1837
8. T. Strick, M.N. Dessinges, G. Charvin, N. Dekker, J.F. Allemand, and D. Bensimon Stretching of macromolecules and proteins Rep Prog Phys 66 1 2003 1 45
9. W. Fraser, and D. Stump The equilibrium of the convergence point in two-strand yarn plying Int J Solid Struct 35 3-4 1998 295 298
10. B. Coleman, and D. Swigon Theory of supercoiled elastic rings with self-contact and its application to DNA plasmids J Elasticity 60 2000 173 221
11. J. Thompson, G. van der Heijden, and S. Neukirch Supercoiling of DNA plasmids: mechanics of the generalized ply Proc R Soc Lond A 458 2020 2002 959 985
12. S. Goyal, N. Perkins, and C. Lee Nonlinear dynamics and loop formation in Kirchhoff rods with implications to the mechanics of DNA and cables J Comput Phys 209 1 2005 371 389
13. S. Goyal, and N. Perkins Looping mechanics of rods and dna with non-homogeneous and discontinuous stiffness Int J Non-Linear Mech 43 2008 1121 1129
14. G. van der Heijden, J. Thompson, and S. Neukirch A variational approach to loaded ply structures J Vib Control 9 1-2 2003 175 185
15. P.K. Purohit Plectoneme formation in twisted fluctuating rods J Mech Phys Solids 56 5 2008 1715 1729
16. Purohit P.K. Shape and energetics of DNA plectonemes. Chapter in IUTAM book series: IUTAM Symposium on Cellular, Molecular and Tissue Mechanics; 2010. ISBN 978-90-481-3347-5.
17. N. Clauvelin, B. Audoly, and S. Neukirch Mechanical response of plectonemic DNA: an analytical solution Macromolecules 41 12 2008 4479 4483
18. N. Clauvelin, B. Audoly, and S. Neukirch Elasticity and electrostatics of plectonemic DNA Biophys J 96 9 2009 3716 3723
19. S. Neukirch, and J. Marko Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA Phys Rev Lett 106 13 2011 138104
20. H. Brutzer, N. Luzzietti, D. Klaue, and R. Seidel Energetics at the DNA supercoiling transition Biophys J 98 7 2010 1267 1276
21. C. Maffeo, S. Robert, H. Brutzer, S. René, A. Aleksei, and W. Gero DNA-DNA interactions in tight supercoils are described by a small effective charge density Phys Rev Lett 105 15 2010 158101
22. B. Daniels, S. Forth, M.Y. Sheinin, D. Wang, and J.P. Sethna Discontinuities at the DNA supercoiling transition Phys Rev E 80 2009 040901 R
23. N. Chouaieb, A. Goriely, and J. Maddocks Helices Proc Natl Acad Sci 103 25 2006 9398 9403
24. G. van der Heijden The static deformation of a twisted elastic rod constrained to lie on a cylinder Proc R Soc Lond A 457 2007 2001 695 715
25. J. Moroz, and P. Nelson Torsional directed walks, entropic elasticity, and DNA twist stiffness Proc Natl Acad Sci 94 26 1997 14418 14422
26. J. Moroz, and P. Nelson Entropic elasticity of twist-storing polymers Macromolecules 31 18 1998 6333 6347
27. A. Stasiak, and J. Maddocks Mathematics. Best packing in proteins and DNA Nature 406 6793 2000 251 253
28. P. Pierański search of ideal knots Series on Knots and everything vol. 19 1998 World Scientific Singapore 20 41
29. J. Coyne Analysis of the formation and elimination of loops in twisted Cable IEEE J Oceanic Eng 15 1990 72 83
30. I.M. Kúlic, H. Mohrbach, R. Thaokar, and H. Schiessel Equation of state of looped DNA Phys Rev E 75 1 2007 011913
31. N.J. Agrawal, R. Radhakrishnan, and P. Purohit Geometry of mediating protein affects the probability of loop formation in DNA Biophys J 94 2008 3150 3158
32. S. Neukirch, and E.L. Starostin Writhe formulas and antipodal points in plectonemic DNA configurations Phys Rev E 78 4 2008 041912
33. J. Ubbink, and T. Odijk Electrostatic-undulatory theory of plectonemically supercoiled DNA Biophys J 76 5 1999 2502 2519
34. A.A. Kornyshev, D.J. Lee, S. Leikin, and A. Wynveen Structure and interactions of biological helices Rev Mod Phys 79 3 2007 943 996
35. S. Brenner, and V. Parsegian A physical method for deriving the electrostatic interaction between rod-like polyions at all mutual angles Biophys J 14 4 1974 327 334
36. R. Podgornik, and V. Parsegian Molecular fluctuations in the packing of polymeric liquid crystals Macromolecules 23 8 1990 2265 2269
37. J. Marko, and E. Siggia Statistical-mechanics of supercoiled DNA Phys Re E 52 3 1995 2912 2938
38. D. Andelman Introduction to electrostatics in soft and biological matter Scottish Graduate Series 2006 Taylor and Francis Boca Raton, FL 97 122
39. J.R.C. van der Maarel Introduction to biopolymer physics 2008 World Scientific Singapore
40. H. Zhang, and J. Marko Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements Phys Rev E 77 3 Pt 1 2008 031916
41. D. Stigter The charged colloidal cylinder with a Gouy double layer J Colloid Interface Sci 53 1975 296
42. D. Stigter Interactions of highly charged colloidal cylinders with applications to double-stranded DNA Biopolymers 16 1977 1435 1448
43. J. Schellman, and D. Stigter Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA Biopolymers 16 1977 1415 1434
44. A. Vologodskii, and N. Cozzarelli Modeling of long-range electrostatic interactions in DNA Biopolymers 35 3 1995 289 296
45. T. Strick, J. Allemand, V. Croquette, and D. Bensimon Twisting and stretching single DNA molecules Prog Biophys Mol Biol 74 1-2 2000 115 140
46. J. Marko Torque and dynamics of linking number relaxation in stretched supercoiled DNA Phys Rev E 76 2 2007 021926
47. Y. Rudoi, and A. Sukhanov Thermodynamic fluctuation within the Gibbs and Einstein approaches Usp Fiz Nauk 43 12 2000 1169 1199
48. L.D. Landau, and E.M. Lifshitz Statistical Physics 3rd ed. 1980 Pergamon Press New York Pt. 1
49. E. Raspaud, D. Durand, and F. Livolant Interhelical spacing in liquid crystalline spermine and spermidine-DNa precipitates Biophys J 88 2005 392 403
50. Y. Burak, G. Ariel, and D. Andelman Competition between condensation of monovalent and multivalent ions in DNA aggregation Curr Opin Colloid Interface Sci 9 2004 53
51. K. Besteman, K. van Eijk, and S. Lemay Charge inversion accompanies DNA condensation by multivalent ions Nat Phys 3 2007 641
52. A. Savelyev, and G. Papoian Inter-DNA electrostatics from explicit solvent molecular dynamics simulations J Am Chem Soc 129 2007 6060 6061
53. B. Todd, V. Parsegian, A. Shirahata, T. Thomas, and D. Rau Attractive forces between cation condensed DNA double helices Biophys J 95 2008 4775 4782
54. P. Sottas, E. Larquet, A. Stasiak, and J. Dubochet Brownian dynamics simulation of DNA condensation Biophys J 77 1999 1858 1870
55. B. Luan, and A. Aksimentiev Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes Soft Matter 6 2010 243 246
56. C.A. Laughton, and S.A. Harris Atomistic simulation of DNA Atomistic simulation of DNA 1 2011 6590 6600
57. Z. Bryant, M. Stone, J. Gore, S.B. Smith, N. Cozzarelli, and C. Bustamante Structural transitions and elasticity from torque measurements on DNA Nature 424 2003 338 341
58. A. Noy, and R. Golestanian The chiriality of DNA: elasticity cross-terms at base-pair level including A-tracts and the influence of ionic strength J Phys Chem B 114 2010 8022 8031
59. C.G. Baumann, S.B. Smith, V.A. Bloomfield, and C. Bustamante Ionic effects on the elasticity of single DNA molecules Proc Natl Acad Sci USA 94 1997 6185 6190
60. Purohit PK, Argudo DE. Plectonemes with non-uniform helical pitch in single molecule DNA experiments. In Proceedings of the 7th European Nonlinear Dynamics Conference (ENOC 2011); 2011. doi:10.3267/ENOC2011Rome.
61. Brewer L. Deciphering the structure of DNA toroids. Intgr Biol 2010;published online doi:10.1039/c0ib00128g.
62. C. Battle, B. van den Broek, M. Noom, J. van Mameren, G. Wuite, and F. MacKintosh Visualizing the formation and collape of DNA toroids Phys Rev E 80 2009 031917