Electrostatic braiding and homologous pairing of DNA double helices

Biophysical Journal

Volumn 101, Issue 4, 2011, Pages 875-884

  Cortini, Ruggero ^a   Kornyshev, Alexei A ^a   Lee, Dominic J ^a   Leikin, Sergey ^b  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ELECTROLYTE; SODIUM CHLORIDE;

ARTICLE; BASE PAIRING; CHEMISTRY; CONFORMATION; DRUG EFFECT; HOMOLOGOUS RECOMBINATION; NUCLEOTIDE SEQUENCE; OSMOLARITY; SEQUENCE HOMOLOGY; STATIC ELECTRICITY; THERMODYNAMICS;

BASE PAIRING; BASE SEQUENCE; DNA; ELECTROLYTES; HOMOLOGOUS RECOMBINATION; NUCLEIC ACID CONFORMATION; OSMOLAR CONCENTRATION; SEQUENCE HOMOLOGY, NUCLEIC ACID; SODIUM CHLORIDE; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 80052472874     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.06.058     Document Type: Article

References (55)

1. A. Barzel, and M. Kupiec Finding a match: how do homologous sequences get together for recombination? Nat. Rev. Genet. 9 2008 27 37 (Pubitemid 350277300)
2. D. Zickler, and N. Kleckner Meiotic chromosomes: integrating structure and function Annu. Rev. Genet. 33 1999 603 754 (Pubitemid 30083134)
3. L. Aragón-Alcaide, and A.V. Strunnikov Functional dissection of in vivo interchromosome association in Saccharomyces cerevisiae Nat. Cell Biol. 2 2000 812 818
4. M. Molnar, and N. Kleckner Examination of interchromosomal interactions in vegetatively growing diploid Schizosaccharomyces pombe cells by Cre/loxP site-specific recombination Genetics 178 2008 99 112 (Pubitemid 351398734)
5. A.A. Kornyshev, and S. Leikin Sequence recognition in the pairing of DNA duplexes Phys. Rev. Lett. 86 2001 3666 3669 (Pubitemid 32416200)
6. G.S. Baldwin, and N.J. Brooks A.A. Kornyshev DNA double helices recognize mutual sequence homology in a protein free environment J. Phys. Chem. B 112 2008 1060 1064 (Pubitemid 351257468)
7. C. Danilowicz, and C.H. Lee M. Prentiss Single molecule detection of direct, homologous, DNA/DNA pairing Proc. Natl. Acad. Sci. USA 106 2009 19824 19829
8. A.G. Cherstvy, A.A. Kornyshev, and S. Leikin Torsional deformation of double helix in interaction and aggregation of DNA J. Phys. Chem. B 108 2004 6508 6518
9. A.A. Kornyshev, and D.J. Lee A. Wynveen Structure and interactions of biological helices Rev. Mod. Phys. 79 2007 943 996 (Pubitemid 47364615)
10. J.C. Wang Cellular roles of DNA topoisomerases: a molecular perspective Nat. Rev. Mol. Cell Biol. 3 2002 430 440 (Pubitemid 34685700)
11. J.C. Wang DNA topoisomerases Annu. Rev. Biochem. 65 1996 635 692 (Pubitemid 26250622)
12. N.R. Cozzarelli DNA gyrase and the supercoiling of DNA Science 207 1980 953 960 (Pubitemid 10103715)
13. Y. Timsit, and P. Várnai Helical chirality: a link between local interactions and global topology in DNA PLoS ONE 5 2010 e9326
14. E. Marguet, and P. Forterre DNA stability at temperatures typical for hyperthermophiles Nucleic Acids Res. 22 1994 1681 1686 (Pubitemid 24155826)
15. D.J. Lee, and A. Wynveen S. Leikin Undulations enhance the effect of helical structure on DNA interactions J. Phys. Chem. B 114 2010 11668 11680
16. R.R. Netz, and H. Orland Variational charge renormalization in charged systems Eur. Phys. J E Soft Matter 11 2003 301 311
17. G. Charvin, and A. Vologodskii V. Croquette Braiding DNA: experiments, simulations, and models Biophys. J. 88 2005 4124 4136 (Pubitemid 40991124)
18. J. Marko Supercoiled and braided DNA under tension Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics 55 1997 1758 1772 (Pubitemid 127607529)
19. T.C. Boles, J.H. White, and N.R. Cozzarelli Structure of plectonemically supercoiled DNA J. Mol. Biol. 213 1990 931 951 (Pubitemid 20213225)
20. T.R. Strick, and J.F. Allemand V. Croquette Behavior of supercoiled DNA Biophys. J. 74 1998 2016 2028 (Pubitemid 28157936)
21. A.G. Cherstvy Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling J. Biol. Phys. 37 2011 227 238
22. N. Clauvelin, B. Audoly, and S. Neukirch Elasticity and electrostatics of plectonemic DNA Biophys. J. 96 2009 3716 3723
23. C. Maffeo, and R. Schöpflin R. Seidel DNA-DNA interactions in tight supercoils are described by a small effective charge density Phys. Rev. Lett. 105 2010 158101
24. J.M. Fogg, and D.J. Catanese L. Zechiedrich Differences between positively and negatively supercoiled DNA that topoisomerases may distinguish C.J. Benham, S. Harvey, W.K. Olson, D.W. Sumners, D. Swigon, Mathematics of DNA Structure, Function and Interactions 2009 Springer New York 73 121
25. A.A. Kornyshev, S. Leikin, and S.V. Malinin Chiral electrostatic interaction and cholesteric liquid crystals of DNA Eur. Phys. J E Soft Matter 7 2002 83 93 (Pubitemid 36185078)
26. P. Várnai, and Y. Timsit Differential stability of DNA crossovers in solution mediated by divalent cations Nucleic Acids Res. 38 2010 4163 4172
27. L. Yakushevich Nonlinear Physics of DNA 2004 Vch Verlagsgesellschaft Mbh Weinheim, Germany
28. A.A. Gorin, V.B. Zhurkin, and W.K. Olson B-DNA twisting correlates with base-pair morphology J. Mol. Biol. 247 1995 34 48
29. J.S. Mitchell, C.A. Laughton, and S.A. Harris Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA Nucleic Acids Res. 39 2011 3928 3938
30. J. DeRouchey, V.A. Parsegian, and D.C. Rau Cation charge dependence of the forces driving DNA assembly Biophys. J. 99 2010 2608 2615
31. D.C. Rau, and V.A. Parsegian Direct measurement of temperature-dependent solvation forces between DNA double helices Biophys. J. 61 1992 260 271
32. D.C. Rau, and V.A. Parsegian Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces Biophys. J. 61 1992 246 259
33. B.A. Todd, and V.A. Parsegian D.C. Rau Attractive forces between cation condensed DNA double helices Biophys. J. 94 2008 4775 4782
34. A.A. Kornyshev, and S. Leikin Theory of interaction between helical molecules J. Chem. Phys. 107 1997 3656 3674
35. P.J. Hagerman Flexibility of DNA Annu. Rev. Biophys. Biophys. Chem. 17 1988 265 286
36. A. Wynveen, and D.J. Lee S. Leikin Helical coherence of DNA in crystals and solution Nucleic Acids Res. 36 2008 5540 5551
37. A.A. Kornyshev, and S. Leikin Electrostatic interaction between long, rigid helical macromolecules at all interaxial angles Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics 62 2 Pt B 2000 2576 2596
38. G.C.L. Wong, and L. Pollack Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins Annu. Rev. Phys. Chem. 61 2010 171 189
39. A.Y. Grosberg, T.T. Nguyen, and B.I. Shklovskii Colloquium: the physics of charge inversion in chemical and biological systems Rev. Mod. Phys. 74 2002 329 345
40. R. Netz, and H. Orland Beyond Poisson-Boltzmann: fluctuation effects and correlation functions Eur. Phys. J E Soft Matter 1 2000 203 214
41. N. Hud Nucleic Acid-Metal Ion Interactions 2009 The Royal Society of Chemistry Cambridge, UK
42. A.A. Kornyshev, and S. Leikin Electrostatic zipper motif for DNA aggregation Phys. Rev. Lett. 82 1999 4138 4141 (Pubitemid 129689381)
43. V.A. Bloomfield DNA condensation Curr. Opin. Struct. Biol. 6 1996 334 341 (Pubitemid 26197433)
44. J. Pelta Jr. , and D. Durand F. Livolant DNA mesophases induced by spermidine: structural properties and biological implications Biophys. J. 71 1996 48 63 (Pubitemid 26227291)
45. J. Pelta, F. Livolant, and J.L. Sikorav DNA aggregation induced by polyamines and cobalthexamine J. Biol. Chem. 271 1996 5656 5662 (Pubitemid 26083901)
46. L. Li, and S.A. Pabit L. Pollack Double-stranded RNA resists condensation Phys. Rev. Lett. 106 2011 108101
47. Y. Bai, and R. Das S. Doniach Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution Proc. Natl. Acad. Sci. USA 102 2005 1035 1040 (Pubitemid 40170721)
48. Y. Timsit, and D. Moras DNA self-fitting: the double helix directs the geometry of its supramolecular assembly EMBO J. 13 1994 2737 2746 (Pubitemid 24191683)
49. Y.C. Xu, and H. Bremer Winding of the DNA helix by divalent metal ions Nucleic Acids Res. 25 1997 4067 4071 (Pubitemid 27443336)
50. J. Gore, and Z. Bryant C. Bustamante DNA overwinds when stretched Nature 442 2006 836 839 (Pubitemid 44258916)
51. J.J. Champoux DNA topoisomerases: structure, function, and mechanism Annu. Rev. Biochem. 70 2001 369 413 (Pubitemid 32662215)
52. N.J. Crisona, and T.R. Strick N.R. Cozzarelli Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements Genes Dev. 14 2000 2881 2892
53. M.D. Stone, and Z. Bryant N.R. Cozzarelli Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases Proc. Natl. Acad. Sci. USA 100 2003 8654 8659 (Pubitemid 36899153)
54. K.C. Neuman, and G. Charvin V. Croquette Mechanisms of chiral discrimination by topoisomerase IV Proc. Natl. Acad. Sci. USA 106 2009 6986 6991
55. G. Charvin, D. Bensimon, and V. Croquette Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases Proc. Natl. Acad. Sci. USA 100 2003 9820 9825 (Pubitemid 37087025)