Physics of DNA: Unravelling hidden abilities encoded in the structure of ' the most important molecule’

Physical Chemistry Chemical Physics

Volumn 12, Issue 39, 2010, Pages 12352-12378

  Kornyshev, Alexei A ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL; ARTICLE; CHEMISTRY; CONFORMATION; GENETIC RECOMBINATION; GENETICS; HUMAN; METABOLISM;

ANIMALS; DNA; HUMANS; NUCLEIC ACID CONFORMATION; RECOMBINATION, GENETIC;

EID: 77957903315     PISSN: 14639076     EISSN: None     Source Type: Journal    
DOI: 10.1039/c004107f     Document Type: Article

References (172)

1. A. Barzel, M. Kupiec, Finding a match: how do homologous sequences get together for recombination?Nat. Rev. Genet., 2008, 9, 27-37
2. D. Zickler, From early homologue recognition to synaptonemal complex formationChromosoma, 2006, 115, 158-174
3. A. A. Kornyshev, S. Leikin, Sequence recognition in the pairing of DNA duplexesPhys. Rev. Lett., 2001, 86, 3666-3669
4. A. A. Kornyshev, S. Leikin, Electrostatic zipper motif for DNA aggregationPhys. Rev. Lett., 1999, 82, 4138-4141
5. A. A. Kornyshev, D. J. Lee, S. Leikin, A. Wynveen, Structure and interactions of biological helicesRev. Mod. Phys., 2007, 79, 943-996
6. V. V. Kushev, Mechanisms of Genetic Recombination, Consultant Bureau, New York, 1974
7. The Recombination of Genetic Material, ed. K. B. Low, Academic Press, San Diego, 1988
8. D. R. F. Leach, Genetic Recombination, Blackwell Science, Oxford, 1996
9. Genetic Recombination Research Progress, ed. J. H. Schulz, Nova Sci. Pbls, New York, 2004
10. Molecular Genetic Recombination, ed. A. Aquilera and R. Rothstein, Springer, Berlin, 2007
11. D. J. Sherratand and S. C. West, Royal Society Discussion (2004) Replicating and reshaping DNA: A celebration of the jubilee of the double helix, Phil. Trans. Royal Soc. B, 2004, p. 359
12. J. Ringo, Funamental Genetics, Cambridge University Press, Cambridge UK, 2004
13. B. Lewin, Genes VI, Oxford University Press, Oxford, 1997
14. F. Madia, et al, Longevity mutation in SCH9 prevents recombination errors and premature genomic stability in a Werner/Bloom model systemJ. Cell Biol., 2008, 180, 67-81
15. B. S. Singer, L. Gold, P. Gauss, D. H. Doherty, Determination of the amount of homology required for recombination in Bacteriophage-T4Cell, 1982, 31, 25-33
16. J. Rubnitz, S. Subramani, The minimum amount of homology required for homologous recombination in mammalian cellsMol. Cell Biol., 1984, 4, 2253-2258
17. V. M. Watt, C. J. Ingles, M. S. Urdea, W. J. Rutter, Homology requirements for recombination in Escherichia-coliProc. Natl. Acad. Sci. U. S. A., 1985, 82, 4768-4772
18. F. Crick, General model for chromosomes of higher organismsNature, 1971, 234, 25-27
19. H. M. Sobell, Molecular mechanism for genetic recombinationProc. Natl. Acad. Sci. U. S. A., 1972, 69, 2483-2487
20. G. G. Doyle, A general theory of chromosome pairing based on the palindromic DNA model of Sobell with modifications and amplificationJ. Theor. Biol., 1978, 70, 171-184
21. R. E. Wagner, M. Radman, A mechanism for initiation of genetic recombinationProc. Natl. Acad. Sci. U. S. A., 1975, 72, 3619-3622
22. D. R. Forsdyke, A stem-loop “kissing” model for the initiation of recombination and the origin of intronsMol. Biol. Evol., 1995, 12, 949-958
23. D. R. Forsdyke, Evolutionary Bioinfiormatics, Springer, New York, 2006
24. R. D. Camerini-Otero, P. Hsieh, Homologous recombination proteins in prokaryotes and eukaryotesAnnu. Rev. Genet., 1995, 29, 509-552
25. B. McClintock, The association of non-homologous parts of chromosomes in the mid-prophase of meiosis inCell Tissue Res., 1933, 19, 191-237
26. S. Henikoff, Nuclear organization and gene expression: Homologous pairing and long-ranged interactionsCurr. Opin. Cell Biol., 1997, 9, 388-395
27. S. Keeney, N. Kleckner, Communication between homologous chromosomes: Genetic alterations at a nuclease-hypersensitive site can altar mitotic chromatin structure at that cite both in cis and in transGenes Cells, 1996, 1, 475-489
28. B. M. Weiner, N. Kleckner, Chromosome pairing via multiple interstitial interactions before and during meiosis in yeastCell, 1994, 77, 977-991
29. S. M. Burgess, N. Kleckner, B. M. Weiner, Somatic pairing of homologs in budding yeast: existence and modulationGenes Dev., 1999, 13, 1627-1641
30. D. Zickler, N. Kleckner, Meiotic chromosomes: integrating structure and functionAnnu. Rev. Genet., 1999, 33, 603-754
31. Later in scientific tabloids this phenomenon, has received a controversial but catchy label: DNA ' telepathy’. This logo grabs attention, but as quotes could be so easily and were often lost, it proved to be misleading for wide public
32. A. A. Kornyshev, S. Leikin, Theory of interaction between helical moleculesJ. Chem. Phys., 1997, 107, 3656-3674
33. A. A. Kornyshev, S. Leikin, Symmetry laws for interaction between helical macromoleculesBiophys. J., 1998, 75, 2513-2519
34. A. A. Kornyshev, S. Leikin, Electrostatic interaction between helical macromolecules in dense aggregates: An impetus for DNA poly- and mesomorphismProc. Natl. Acad. Sci. U. S. A., 1998, 95, 13579-13584
35. “DNA need not unzip” 2001 Physical Review Focus http://focus.aps.org/v7/st19.html
36. W. K. Olson, V. B. Zhurkin, Modeling DNA deformationsCurr. Opin. Struct. Biol., 2000, 10, 286-297
37. A. G. Cherstvy, A. A. Kornyshev, S. Leikin, Torsional deformation of double helix in interaction and aggregation of DNAJ. Phys. Chem. B, 2004, 108, 6508-6518
38. A. A. Kornyshev, A. Wynveen, Nonlinear effects in the torsional adjustment of interacting DNAPhys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2004, 69, 041905.
39. A. Wynveen, D. J. Lee, A. A. Kornyshev, S. Leikin, Helical coherence of DNA in crystals and solutionNucleic Acids Res., 2008, 36, 5540-5551
40. J. Widom, R. L. Baldwin, Cation-induced toroidal condensation of DNA. Studies with cobalt hexaminJ. Mol. Biol., 1980, 144, 431-453
41. D. Lang, Regular superstructures of purified DNA in ethanolic solutionsJ. Mol. Biol., 1973, 78, 247-253
42. D. Lang, T. N. Taylor, D. C. Dobyan, D. M. Gray, circular DNA-electron-microscopy of ethanol-condensed moleculesJ. Mol. Biol., 1976, 106, 97-107
43. T. H. Eickbush, E. N. Moudrianakis, Compaction of DNA helices into either continuous supercoils or folded-fiber rods and toroidsCell, 1978, 13, 295-306
44. D. K. Chattoraj, L. C. Gosule, J. A. Schellman, DNA condensation with polyaminesJ. Mol. Biol., 1978, 121, 327-337
45. K. A. Marx, G. C. Ruben, Evidence for hydrated spermidine calf thymus DNA toruses organized by circumferential dna wrappingNucleic Acids Res., 1983, 11, 1839-1854
46. P. G. Arscott, A. Z. Li, V. A. Bloomfield, Condensation of DNA by trivalent cations. 1. effects of DNA length and topology on the size and shape of condensed particlesBiopolymers, 1990, 30, 619-630
47. N. V. Hud, I. D. Vilfan, Toroidal DNA condensates: Unraveling the fine structure and the role of nucleation in determining sizeAnnu. Rev. Biophys. Biomol. Struct., 2005, 34, 295-318
48. C. Robinson, Liquid-crystalline structures in polypeptide solutionsTetrahedron, 1961, 13, 219-226
49. R. L. Rill, P. R. Hilliard Jr., G. C. Levy, Spontaneous ordering of DNAJ. Biol. Chem., 1983, 258, 250-256
50. + DNAProc. Natl. Acad. Sci. U. S. A., 1986, 83, 342-346
51. J. L. Sikorav, J. Pelta, F. Livolant, A liquid crystalline phase in spermidine-condensed DNABiophys. J., 1994, 67, 1387-1392
52. F. Livolant, A. Leforestier, Condensed phases of DNA: structures and phase transitionsProg. Polym. Sci., 1996, 21, 1115-1164
53. J. Pelta, F. Livolant, J.-L. Sikorav, DNA aggregation induced by polyamines and cobalthexamineJ. Biol. Chem., 1996, 271, 5656-5662
54. R. Podgornik, H. H. Strey, K. Gawrisch, D. C. Rau, A. Rupprecht, V. A. Parsegian, Bond orientational order, molecular motion and free energy of high-density DNA mesophasesProc. Natl. Acad. Sci. U. S. A., 1996, 93, 4261-4624
55. H. H. Strey, J. Wang, R. Podgornik, A. Rupprecht, L. Yu, V. A. Parsegian, E. B. Sirota, Refusing to Twist: Demonstration of a Line Hexatic Phase in DNA Liquid CrystalsPhys. Rev. Lett., 2000, 84, 3105-3108
56. E. Raspaud, D. Durand, F. Livolant, Interhelical spacing in liquid crystalline spermine and spermidine-DNA precipitatesBiophys. J., 2005, 88, 392-403
57. N. Sartori Blanc, A. Senn, A. Leforestier, F. Livolant, J. Dubochet, DNA in human and stallion spermatazoa forms local hexagonal packing with twist and many defectsJ. Struct. Biol., 2001, 134, 76-81
58. A. Leforestier, F. Livolant, Structure of toroidal DNA collapsed inside the phage capsidProc. Natl. Acad. Sci. U. S. A., 2009, 106, 9157-9162
59. M. A. Krasnow, N. R. Cozzarelli, Catenation of DNA. Rings by TopoisomerasesJ. Biol. Chem., 1982, 257, 2687-2693
60. J. L. Sikorav, G. M. Church, Complementary recognition in condensed DNA: accelerated DNA renaturationJ. Mol. Biol., 1991, 222, 1085-1108
61. E. Raspaud, I. Chaperon, A. Leforestier, F. Livolant, Spermine-induced aggregation of DNA, nucleosome and chromatinBiophys. J., 1999, 77, 1547-1555
62. V. A. Bloomfield, DNA condensationCurr. Opin. Struct. Biol., 1996, 6, 334-341
63. P. Saccardo, A. Villaverde, Gonzalez-Montalban N Peptide-mediated DNA condensation for non-viral gene therapyBiotechnol. Adv., 2009, 27, 432-438
64. H. Deng, V. A. Bloomfield, Structural effects of cobalt-amine compounds on DNA condensationBiophys. J., 1999, 77, 1556-1561
65. D. A. Knoll, M. G. Fried, and V. A. Bloomfield, Heat-induced DNA aggregation in the presence of divalent metal salts, in Structure and Expression: DNA and its Drug Complexes, ed. R. H. Sarma and M. H. Sarma, Adenine Press, Albany, NY, 1988, pp. 123-145
66. D. C. Rau, V. A. Parsegian, Direct measurement of temperature-dependent solvation forces between DNA double helicesBiophys. J., 1992, 61, 260-271
67. S. Leikin, D. C. Rau, V. A. Parsegian, Direct measurement of forces between self-assembled proteins: temperature-dependent exponential forces between collagen triple helicesProc. Natl. Acad. Sci. U. S. A., 1994, 91, 276-280
68. A. A. Zinchenko, V. G. Sergeyev, K. Yamabe, S. Murata, K. Yoshikawa, Stereoisomeric Discrimination in DNA CompactionChemBioChem, 2004, 5, 360-368
69. V. Vijayanathan, T. Thomas, A. Shirahata, T. J. Thomas, DNA condensation by polyamines: a laser light scattering study of structural effectsBiochemistry, 2001, 40, 13644-14651
70. R. W. Wilson, V. A. Bloomfield, Counterion-induced condesation of deoxyribonucleic acid. A light scattering studyBiochemistry, 1979, 18, 2192-2196
71. J. Widom, R. L. Baldwin, Monomolecular condensation of lambda-DNA induced by cobalt hexamineBiopolymers, 1983, 22, 1595-1620
72. D. Matulis, I. Rouzina, V. A. Bloomfield, Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanismJ. Mol. Biol., 2000, 296, 1053-1063
73. D. Baigl, K. Yoshikawa, Dielectric control of counterion-induced single-chain folding transition of DNABiophys. J., 2005, 88, 3486-3493
74. N. V. Hud, Double-stranded DNA organization in bacteriophage heads-an alternative toroid-based modelBiophys. J., 1995, 69, 1355-1362
75. J. A. Schellman, N. Parthasarathy, X-ray diffraction studies on cation-collapsed DNAJ. Mol. Biol., 1984, 175, 313-329
76. N. V. Hud, K. H. Downing, Cryoelectron microscopy of λ-phage DNA condensates in vitreous ice: The fine Structure of DNA toroidsProc. Natl. Acad. Sci. U. S. A., 2001, 98, 14925-14930
77. Y. Levin, Electrostatic correlations: from plasma to biologyRep. Prog. Phys., 2002, 65, 1577-1632
78. M. D. Frank-Kamenetskii, V. V. Anshelevich, A. V. Lukashin, Polyelectrolyte model of DNAUsp. Fiz. Nauk., 1987, 151, 595-618
79. A. Yu. Grosberg, T. T. Nguyen, B. I. Shklovskii, The physics of charge inversion in chemical and biological systemsRev. Mod. Phys., 2002, 74, 329-345
80. E. Raspaud, M. Olvera de la Cruz, J. L. Sikorav, F. Livolant, Precipitation of DNA by polyamines: a polyelectrolyte behaviorBiophys. J., 1998, 74, 381-393
81. M. Saminathan, T. Antony, A. Shirahata, L. H. Sigal, T. Thomas, T. J. Thomas, Ionic and structural specificity effects of natural and synthetic polyamines on the aggregation and resolubilization of single-double- and triple-stranded DNABiochemistry, 1999, 38, 3821-3830
82. C. Hsiao, M. Tannenbaum, H. Van Deusen, E. Hershkovitz, G. Perng, A. Tannenbaum, and L. D. Williams, in Nucleic Acid Metal Interactions, ed. N. Hud, RSC, London, 2008, pp.1-35
83. J. Ruiz-Chica, M. A. Medina, F. Sánchez-Jiménez, F. J. Ramírez, On the interpretation of Raman spectra of 1-aminooxy-spermine/DNA complexesNucleic Acids Res., 2004, 32, 579-589
84. A. Ouameur, H.-A. Tajmir-Riahi, Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(iii)hexamine Studied by Fourier Transform Infrared and Capillary ElectrophoresisJ. Biol. Chem., 2004, 279, 42041-42054
85. E. Wemmer, K. S. Srivenugopal, B. R. Reid, D. R. Morris, Nuclear magnetic resonance studies of polyamine binding to a defined DNA sequenceJ. Mol. Biol., 1985, 185, 457-459
86. B. I. Shklovskii, Wigner crystal model of counterion induced bundle formation of rod-like polyelectrolytesPhys. Rev. Lett., 1999, 82, 3268-3271
87. B. I. Shklovskii, Screening of a macroion by multivalent ions: Correlation-induced inversion of chargePhys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top., 1999, 60, 5802-5811
88. T. T. Nguyen, A. Y. Grosberg, B. I. Shklovskii, Macroions in salty water with multivalent ions: Giant inversion of chargePhys. Rev. Lett., 2000, 85, 1568-1571
89. T. T. Nguyen, I. Rouzina, B. I. Shklovskii, Reentrant condensation of DNA induced by multivalent counterionsJ. Chem. Phys., 2000, 112, 2562-2568
90. J. Yang, D. C. Rau, Incomplete ion dissociation underlies the weakened attraction between DNA helices at high spermidine concentrationsBiophys. J., 2005, 89, 1932-1940
91. S. A. Allison, J. C. Herr, J. M. Schurr, Structure of viral DNA condensed by simple triamines: A light-scattering and electron-microscopy studyBiopolymers, 1981, 20, 469-488
92. V. A. Bloomfield, D. M. Crothers, and I. Tinoco Jr, Nucleic Acids: Structures, Properties and Functions, University Science Books, Sausalito, California, 2000
93. F. Oosawa, Polyelectrolytes, Marcel Dekker, New York, 1971
94. R. Marquet, C. Houssier, Thermodynamics of cation-induced DNA condensationJ. Biomol. Struct. Dyn., 1991, 9, 159-167
95. J. J. Arenzon, J. F. Stilck, Y. Levin, Simple Model for Attraction between. Like-Charged PolyionsEur. Phys. J. B, 1999, 12, 79-82
96. B.-Y. Ha, A. J. Liu, Counterion-mediated, non-pairwise additive attractions in bundles of like-charged rodsPhys. Rev. E: Stat.Phys., Plasmas, Fluids, Relat. Interdiscip. Top., 1999, 60, 803-813
97. I. Rouzina, V. A. Bloomfield, Macroion attraction due to electrostatic correlation between screening counterions. I: mobile surface-adsorbed ions and diffuse ion cloudJ. Phys. Chem., 1996, 100, 9977-9989
98. M. S. Loth, B. I. Shklovskii, Non-mean-field screening by multivalent counterionsJ. Phys.: Condens. Matter, 2009, 21, 424104.
99. E. P. Wigner, On the interaction of electrons in metalsPhys. Rev., 1934, 46, 1002-1011
100. B. Tanatar, D. M. Ceperley, Ground state of the two-dimensional electron gasPhys. Rev. B: Condens. Matter, 1989, 39, 5005-5016
101. T. Ando, A. B. Fowler, F. Stern, Electronic properties of two-dimensional systemsRev. Mod. Phys., 1982, 54, 437-672
102. M. A. Vorotyntsev, S. N. Ivanov, Statistical mechanics of an ion ensemble adsorbed at a meteal/dielectric interfaceZh. Exper.Theor. Fiz., 1985, 88, 1729-1737
103. M. E. Leunissen, A. van Blaadern, A. D. Hollingsworth, M. T. Sullivan, P. M. Chaikin, Electrostatics at the oil-water interface, stability, and order in emulsions and colloidsProc. Natl. Acad. Sci. U. S. A., 2007, 104, 2585-2590
104. N. D. Mermin, H. Wagner, “Absence of Ferromagnetism or Antiferromagnetism in One- or Two-Dimensional Isotropic Heisenberg Models”Phys. Rev. Lett., 1966, 17, 1133-1136
105. A. Klein, L. J. Landau, D. S. Shucker, On the absence of spontaneous breakdown of continuous symmetry for equilibrium states in two dimensions”J. Stat. Phys., 1981, 26, 505-512
106. M. Deserno, C. Holm, Theory and simulations of rigid polyelectrolytesMol. Phys., 2002, 100, 2941-2956
107. A. G. Cherstvy, A. A. Kornyshev, S. Leikin, Temperature dependent DNA condensation triggered by rearrangements of adsorbed ionsJ. Phys. Chem. B, 2002, 106, 13362-13369
108. G. S. Manning, The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotidesQ. Rev. Biophys., 1978, 11, 179-246
109. K Bryson, R. J. Greenall, Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealingJ. Biomol. Struct. Dyn., 2000, 18, 393-412
110. B. G. Feuerstein, N. Pattabiraman, L. J. Marton, Spermine-DNA interactions: a theoretical studyProc. Natl. Acad. Sci. U. S. A., 1986, 83, 5948-5952
111. A. P. Lyubartsev, A. Laaksonen, Molecular Dynamics Simulations of DNA in Solution with Different CounterionsJ. Biomol. Struct. Dyn., 1998, 16, 579-587
112. N. Korolev, A. P. Lyubartsev, L. Nordenskiöld, A. Laaksonen, Spermine: An “invisible” component in the crystals of B-DNA: A grand canonical Monte Carlo and Molecular Dynamics simulation studyJ. Mol. Biol., 2001, 308, 907-917
113. N. Korolev, A. P. Lyubartsev, A. Laaksonen, L. Nordenskiöld, On the competition between water, sodium ions and spermine in binding to DNA. A molecular dynamics computer simulation studyBiophys. J., 2002, 82, 2860-2875
114. N. Korolev, A. P. Lyubartsev, A. Laaksonen, L. Nordenskiöld, A molecular dynamics simulation study of polyamine and sodium DNA. Interplay between polyamine binding and DNA structureEur. Biophys. J., 2004, 33, 671-682
115. + with condensed ordered DNA. A molecular dynamics computer simulation studyNucleic Acids Res., 2006, 34, 686-696
116. L. Dai, Y. Mu, L. Nordenskiold, A. Lapp, J. R. C. van der Maarel, Charge Structure and Counterion Distribution in Hexagonal DNA Liquid CrystalBiophys. J., 2007, 92, 947-958
117. A. Falaschi, Similia similibus: pairing of homologous chromosomes driven by the physicochemical properties of DNAHFSP J., 2008, 2, 257-261
118. G. Baldwin, N. J. Brooks, R. Robson, A. Wynveen, A. Goldar, S. Leikin, J. M. Seddon, A. A. Kornyshev, DNA double helices recognize mutual sequence homology in a protein-free environmentJ. Phys. Chem. B, 2008, 112, 1060-1064
119. L. D. Landau, and E. M. Lifshitz, Electrodynamics of continuous media, Course of Theoretical Physics, Oxford, Pergamon, 2nd edn, 1984, vol. 8
120. B. A. Todd, V. A. Parsegian, A. Shirata, T. J. Thomas, D. C. Rau, Attractive forces between cation condensed double helicesBiophys. J., 2008, 94, 4775-4782
121. Yu. A. Izyumov, and Yu. N. Skryabin, Statistical Theory of Magnetically Ordered Systems, Consultants Bureau, New York, 1988, p. 295
122. H. M. Harreis, A. A. Kornyshev, C. N. Likos, H. Loewen, G. Sutmann, Phase behavior of columnar DNA assembliesPhys. Rev. Lett., 2002, 89, 18303-18207
123. A. Wynveen, D. J. Lee, A. A. Kornyshev, Statistical mechanics of columnar DNA assembliesEur. Phys. J. E, 2005, 16, 303-318
124. A. A. Kornyshev, S. Leikin, Electrostatic Interaction between long, rigid helical molecules at all mutual anglesPhys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top., 2000, 62, 2576-2596
125. A. A. Kornyshev, S. Leikin, S. V. Malinin, Chiral interaction and cholesteric liquid crystals of DNAEur. Phys. J. E, 2002, 7, 83-93
126. C. B. Stanley, H. Hong, H. H. Strey, DNA cholesteric pitch as a function of density and ionic strengthBiophys. J., 2005, 89, 2552-2557
127. A. A. Kornyshev, D. J. Lee, S. Leikin, A. Wynveen, S. Zimmerman, Direct observation of azimuthal correlations between DNA in hydrated aggregatesPhys. Rev. Lett., 2005, 95, 14, 148102-4
128. L. Rudd, D. J. Lee, A. A. Kornyshev, The role of electrostatics in the B to A transition of DNA: from solution to assemblyJ. Phys.: Condens. Matter, 2007, 19, 416103.
129. W. Gilbert, The RNA WorldNature, 1986, 319, 618.
130. C. Woese, The Genetic Code, Harper & Row, New York, 1968
131. L. E. Orgel, The origin of life on the EarthSci. Am., 1994, 271, 76-83
132. L. E. Orgel, The origin of life-a review of facts and speculationsTrends Biochem. Sci., 1998, 23, 491-495
133. Ed. R. F. Gesterland, T. Chech, and J. F. Atkins, The RNA World, III Edition, 2006, Cold Spring Harbour Laboratory Press, New York
134. W. M. Gelbart, C. M. Knobler, Pressurized VirusesScience, 2009, 323, 1682-1683
135. A. Evilevitch, L. Lavelle, C. M. Knobler, E. Raspaud, W. M. Gelbart, Osmotic pressure inhibition of DNA ejection from phageProc. Natl. Acad. Sci. U. S. A., 2003, 100, 9292-9295
136. P. K. Purohit, J. Kondev, R. Phillips, Mechanics of DNA packaging in virusesProc. Natl. Acad. Sci. U. S. A., 2003, 100, 3173-3178
137. W. K. Olson, V. B. Zhurkin, Modeling DNA deformationsCurr. Opin. Struct. Biol., 2000, 10, 286-297
138. A. A. Kornyshev, D. J. Lee, A. Wynveen, S. Leikin X-ray diffraction from real DNA (in preparation), 2010
139. A. A. Kornyshev, A. Wynveen, The homology recognition well as an innate property of DNA structureProc. Natl. Acad. Sci. U. S. A., 2009, 106, 4683-4688
140. D. J. Lee, A. A. Kornyshev, Homology recognition funnelJ. Chem. Phys., 2009, 131, 155104.
141. D. J. Lee, A. A. Kornyshev, ErratumJ. Chem. Phys., 2009, 131, 219901.
142. At interaxial separations shorter than R* one can obtain the expression for the force by differentiation of eqn B.5 of ref. 136 with minimization of the optimal azimuthal angle as described there [note a rather obvious misprint in eqn B5: the argument of the second cosine should have a factor of 2, lost in print]. The resulting expression is too cumbersome to be drawn here
143. D. J. Lee, S. Leikin, A. Wynveen, Fluctuations and interactions of semi-flexible polyelectrolytes in columnar assembliesJ. Phys.: Condens. Matter, 2010, 22, 072202.
144. D. J. Lee, A. Wynveen, A. A. Kornyshev, S. Leikin, Undulations enhance the effect of helical structure on DNA interactions submitted toJ. Phys. Chem. B, 2010, in press
145. R. R. Sinden, DNA Structure and Function, Academic Press, Sand Diego, 1994
146. L. Postow, N. J. Crisona, B. J. Peter, C. D. Hardy, N. R. Cozzarelli, Topological challenges to DNA replication: Conformations at the forkProc. Natl. Acad. Sci. U. S. A., 2001, 98, 8219-8226
147. Z. Bryant, M. D. Stone, J. Gore, S. B. Smith, N. R. Cozzarelli, C. Bustamante, Structural transitions and elasticity from torque measurements on DNANature, 2003, 424, 338-341
148. B. J. Peter, J. Arsuaga, A. M. Breier, A. B. Khodursky, P. O. Brown, N. R. Cozzarelli, Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coliGenome Biol., 2004, 5, R87.
149. L. S. Shlyakhtenko, L. Miloseska, V. N. Potaman, R. R. Sinden, Y. I. Lyubchenko, Intersegmental interactions in supercoiled DNA: atomic force microscopy studyUltramicroscopy, 2003, 97, 263-270
150. Z. R. Liu, R. W. Deibler, H. S. Chan, L. Zechiedrich, The why and how of DNA unlinkingNucleic Acids Res., 2009, 37, 661-671
151. M. E. Fisher, The story of coulombic criticalityJ. Stat. Phys., 1994, 75, 1-36
152. D. J. Lee, Charge renormalization of helical macromoleculesJ. Phys.: Condens. Matter, 2010, in press
153. F. Oosawa, A theory on the effect of low molecular salts on the dissociation of linear polyacidsBiopolymers, 1968, 6, 134-144
154. M. Kanduc, J. Dobnikar, R. Podgornik, Counterion-mediated electrostatic interactions between helical moleculesSoft Matter, 2009, 5, 868-877
155. Spooky attraction of DNA from a distance, New Scientist, 2008, 2641, 15
156. G. Crabtree, Paired pairsNature, 2008, 451, 609.
157. P. Szuromi, DNA’s self regardScience, 2008, 319, 879.
158. Seeking recognition, Biopolymers, 2008, 89, 4.
159. C. Q. Choi, Double-Helix Double Up, Scientific American, 2008, April, 30
160. S. Inoue, S. Sugiyama, A. A. Travers, T. Ohyama, Self-assembly of double-stranded DNA molecules at nanomolar concentrationsBiochemistry, 2007, 46, 164-171
161. Z. Liu, H. Zhou, G. Wei, Y. Song, L. Wang, Immobilization and condensation of DNA with 3-aminopropyltriethoxysilane studied by atomic force microscopyJ. Microsc., 2005, 218, 233-239
162. C. Danilovicz, C. H. Lee, K. Kim, K. Hatch, V. W. Coljee, N. Kleckner, M. Prentiss, Single molecule detection of direct, homologous, DNA/DNA pairingProc. Natl. Acad. Sci. U. S. A., 2009, 106, 19824-19829
163. V. A. Parsegian, Harness the hubris: Useful things physicists could do in biologyPhys. Today, 1997, 50, 23-27
164. A. A. Kornyshev, How physics can inspire biologyPhysics World, 2009, 22, 16-17
165. W. Cochran, F. H. C. Crick, V. Vand, The structure of synthetic polypeptides. I. The transform of atoms on a helixActa Crystallogr., 1952, 5, 581-586
166. R. E. Franklin, R. G. Gosling, Molecular configuration in sodium thymonucleateNature, 1953, 171, 740-741
167. R. E. Franklin, R. G. Gosling, Evidence for 2-chain helix in crystalline structure of sodium deoxyribonucleateNature, 1953, 172, 156-157
168. J. D. Watson, F. H. C. Crick, Molecular structure of nucleic acids - a structure for deoxyribose nucleic acidNature, 1953, 171, 737-738
169. J. D. Watson, F. H. C. Crick, Genetical implications of the structure of deoxyribonucleic acidNature, 1953, 171, 964-967
170. M. D. Frank-Kamenetskii, Unravelling DNA: The Most Important Molecule of Life, VCH, Cambridge, 1993
171. Sequence-dependent variations in the local helical pitch H will disrupt such register in juxtaposition of molecules with different sequences but not in juxtaposition of molecules with the same sequences as illustrated in Fig. 5.
172. D. C. Rau, B. Lee, V. A. Parsegian, Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helicesProc. Natl. Acad. Sci. U. S. A., 1984, 81, 2621-2625