DNA curvature and flexibility in vitro and in vivo

Quarterly Reviews of Biophysics

Volumn 43, Issue 1, 2010, Pages 23-63

  Peters, Justin P ^a   Maher, L James ^a  

^a MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN;

ANIMAL; ARTICLE; BASE PAIRING; CHEMISTRY; CONFORMATION; GENETICS; HUMAN; METABOLISM; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; SPECTROSCOPY; STATIC ELECTRICITY;

ANIMALS; BASE PAIRING; BASE SEQUENCE; DNA; DNA-BINDING PROTEINS; HUMANS; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; SPECTRUM ANALYSIS; STATIC ELECTRICITY;

EID: 77957240284     PISSN: 00335835     EISSN: 14698994     Source Type: Journal    
DOI: 10.1017/S0033583510000077     Document Type: Article

References (232)

1. AKI, T. & ADHYA, S. (1997). Repressor induced sitespecific binding of HU for transcriptional regulation. EMBO Journal 16(12), 3666-3674. (Pubitemid 27250059)
2. ALLEMAND, J. F., COCCO, S., DOUARCHE, N. & LIA, G. (2006). Loops in DNA: an overview of experimental and theoretical approaches. European Physical Journal E, Soft Matter 19(3), 293-302.
3. ANSARI, A. & HAMPSEY, M. (2005). A role for the CPF 3kend processing machinery in RNAP II-dependent gene looping. Genes and Development 19(24), 2969-2978. (Pubitemid 41798113)
4. ARIEL, G. & ANDELMAN, D. (2003). Persistence length of a strongly charged rodlike polyelectrolyte in the presence of salt. Physical Reviews E, Statistical, Nonlinear, and Soft Matter Physics 67(1 Pt 1), 11805-11814.
5. BALAEFF, A., MAHADEVAN, L. & SCHULTEN, K. (2004). Structural basis for cooperative DNA binding by CAP and lac repressor. Structure 12(1), 123-132. (Pubitemid 38114812)
6. BAUMANN, C. G., SMITH, S. B., BLOOMFIELD, V.A. & BUSTAMANTE, C. (1997). Ionic effects on the elasticity of single DNA molecules. Proceedings of the National Academy of Sciences USA 94(12), 6185-6190. (Pubitemid 27270659)
7. BECKER, N. A., KAHN, J.D. & MAHER, L. J. III (2005). Bacterial repression loops require enhanced DNA flexibility. Journal of Molecular Biology 349(4), 716-730.
8. BECKER, N. A., KAHN, J.D. & MAHER, L. J. III (2007). Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli. Nucleic Acids Research 35(12), 3988-4000.
9. BECKER, N. A., KAHN, J.D. & MAHER, L. J. III (2008). Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation. Nucleic Acids Research 36(12), 4009-4021.
10. BEDNAR, J., FURRER, P., STASIAK, A., DUBOCHET, J., EGELMAN, E.H. & BATES, A. D. (1994). The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. Journal of Molecular Biology 235(3), 825-847. (Pubitemid 124001697)
11. BELLOMY, G., MOSSING, M. & RECORD, M. (1988). Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process. Biochemistry 27, 3900-3906.
12. BENNETT, M.D. & LEITCH, I. J. (2005). Genome size evolution in plants. In The Evolution of the Genome (ed. T. R. Gregory), pp. 89-162. San Diego: Elsevier.
13. BEVERIDGE, D. L., BARREIRO, G., BYUN, K. S., CASE, D. A., CHEATHAM, T. E. III, DIXIT, S. B., GIUDICE, E., LANKAS, F., LAVERY, R., MADDOCKS, J. H., OSMAN, R., SEIBERT, E., SKLENAR, H., STOLL, G., THAYER, K. M., VARNAI, P. & YOUNG, M. A. (2004). Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophysical Journal 87(6), 3799-3813. (Pubitemid 39602887)
14. BEVERIDGE, D. L., YOUNG, M.A. & SPROUS, D. (1998). Modeling of DNA via molecular dynamics simulation: structure, bending, and conformational transitions. In Molecular Modeling of Nucleic Acids (eds. N. B. Leontis and J. Santa Lucia), pp. 260-284. Washington, DC: American Chemical Society. (Pubitemid 128436660)
15. BHAUMIK, S.R. & GREEN, M. R. (2001). SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Genes & Development 15, 1935-1945.
16. BIANCHI, M. E. (1994). Prokaryotic HU and eukaryotic HMG1: a kinked relationship. Molecular Microbiology 14(1), 1-5.
17. BINTU, L., BUCHLER, N. E., GARCIA, H. G., GERLAND, U., HWA, T., KONDEV, J. & PHILLIPS, R. (2005). Transcriptional regulation by the numbers: models. Current Opinion in Genetics and Development 15(2), 116-124. (Pubitemid 40410659)
18. BLOOMFIELD, V. A. (1997). DNA condensation by multivalent cations. Biopolymers 44(3), 269-282. (Pubitemid 127583675)
19. BOLSHOY, A., MCNAMARA, P., HARRINGTON, R.E. & TRIFONOV, E. N. (1991). Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proceedings of the National Academy of Sciences USA 88, 2312-2316. (Pubitemid 21916406)
20. BROWER-TOLAND, B. D., SMITH, C. L., YEH, R. C., LIS, J. T., PETERSON, C.L. & WANG, M. D. (2002). Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proceedings of the National Academy of Sciences USA 99(4), 1960-1965.
21. BURATOWSKI, S. (1994). The basics of basal transcription by RNA polymerase II. Cell 77, 1-3. (Pubitemid 24184679)
22. BUSTAMANTE, C., SMITH, S. B., LIPHARDT, J. & SMITH, D. (2000). Single-molecule studies of DNA mechanics. Current Opinion in Structural Biology 10(3), 279-285. (Pubitemid 30333096)
23. BUSTIN, M. (2001). Revised nomenclature for high mobility group (HMG) chromosomal proteins. Trends in Biochemical Science 26(3), 152-153. (Pubitemid 32197573)
24. CACCHIONE, S., DE SANTIS, P., FOTI, D., PALLESCHI, A. & SAVINO, M. (1989). Periodical polydeoxynucleotides and DNA curvature. Biochemistry 28(22), 8706-8713. (Pubitemid 19278528)
25. CALLADINE, C. R., DREW, H.R. & MCCALL, M. J. (1988). The intrinsic curvature of DNA in solution. Journal of Molecular Biology 201(1), 127-137.
26. CANTOR, C. & SCHIMMEL, P. (1980). Biophysical Chemistry Part III: The Behavior of Biological Macromolecules. New York: W. H. Freeman.
27. CASERTA, M., AGRICOLA, E., CHURCHER, M., HIRIART, E., VERDONE, L., DI MAURO, E. & TRAVERS, A. (2009). A translational signature for nucleosome positioning in vivo. Nucleic Acids Research 37(16), 5309-5321.
28. CLOUTIER, T.E. & WIDOM, J. (2004). Spontaneous sharp bending of double-stranded DNA. Molecular Cell 14(3), 355-362. (Pubitemid 38591406)
29. CLOUTIER, T.E. & WIDOM, J. (2005). DNA twisting flexibility and the formation of sharply looped protein-DNA complexes. Proceedings of the National Academy of Sciences USA 102(10), 3645-3650. (Pubitemid 40354665)
30. CLUZEL, P., LEBRUN, A., HELLER, C., LAVERY, R., VIOVY, J. L., CHATENAY, D. & CARON, F. (1996). DNA: an extensible molecule. Science 271(5250), 792-794. (Pubitemid 26058929)
31. COHEN, A.E. & MOERNER, W. E. (2005). Method for trapping and manipulating nanoscale objects in solution. Applied Physics Letters 86(9), 093109.
32. CRICK, F.H. & KLUG, A. (1975). Kinky helix. Nature 255(5509), 530-533.
33. CROTHERS, D. M. (1993). Architectural elements in nucleoprotein complexes. Current Biology 3(10), 675-676.
34. CROTHERS, D.M. & DRAK, J. (1992). Global features of DNA structure by comparative gel electrophoresis. Methods in Enzymology 212, 46-71.
35. CROTHERS, D. M., DRAK, J., KAHN, J.D. & LEVENE, S.D. (1992). DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods in Enzymology 212, 3-29.
36. CROTHERS, D. M., HARAN, T.E. & NADEAU, J. G. (1990). Intrinsically bent DNA. Journal of Biological Chemistry 265, 7093-7096. (Pubitemid 20162434)
37. CURUKSU, J., ZACHARIAS, M., LAVERY, R. & ZAKRZEWSKA, K. (2009). Local and global effects of strong DNA bending induced during molecular dynamics simulations. Nucleic Acids Research 37(11), 3766-3773.
38. CZAPLA, L., SWIGON, D. & OLSON, W. K. (2006). Sequencedependent effects in the cyclization of short DNA. Journal of Chemical Theory and Computation 2(3), 685-695.
39. CZAPLA, L., SWIGON, D. & OLSON, W. K. (2008). Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations. Journal of Molecular Biology 382, 353-370.
40. DEHASETH, P. L., LOHMAN, T.M. & RECORD, JR., M. T. (1977). Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release. Biochemistry 16(22), 4783-4790.
41. DEKKER, J., RIPPE, K., DEKKER, M. & KLECKNER, N. (2002). Capturing chromosome conformation. Science 295(5558), 1306-1311. (Pubitemid 34157624)
42. DEMURTAS, D., AMZALLAG, A., RAWDON, E. J., MADDOCKS, J. H., DUBOCHET, J. & STASIAK, A. (2009). Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles. Nucleic Acids Research 37(9), 2882-2893.
43. DICKERSON, R. E., GOODSELL, D. & KOPKA, M. L. (1996). MPD and DNA bending in crystals and in solution. Journal of Molecular Biology 256(1), 108-125. (Pubitemid 26104213)
44. DIXIT, S. B., BEVERIDGE, D. L., CASE, D. A., CHEATHAM, T. E., GIUDICE, E., LANKAS, F., LAVERY, R., MADDOCKS, J. H., OSMAN, R., SKLENAR, H., THAYER, K.M. & VARNAI, P. (2005). 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(6), 3721-3740. (Pubitemid 41725597)
45. DOBI, K. C. & WINSTON, F. (2007). Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Molecular and Cellular Biology 27(15), 5575-5586. (Pubitemid 47124409)
46. DONG, Q., STELLWAGEN, E. & STELLWAGEN, N. C. (2009). Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry 48(5), 1047-1055.
47. DOUARCHE, N. & COCCO, S. (2005). Protein-mediated DNA loops: effects of protein bridge size and kinks. Physical Reviews E, Statistical, Nonlinear, and Soft Matter Physics 72(6 Pt 1), 061902. (Pubitemid 41777631)
48. DREW, H. R. & TRAVERS, A. A. (1985). DNA bending and its relation to nucleosome positioning. Journal of Molecular Biology 186, 773-790.
49. DU, Q., KOTLYAR, A. & VOLOGODSKII, A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Research 36(4), 1120-1128. (Pubitemid 351330930)
50. DU, Q., SMITH, C., SHIFFELDRIM, N., VOLOGODSKAIA, M. & VOLOGODSKII, A. (2005). Cyclization of short DNA fragments and bending fluctuations of the double helix. Proceedings of the National Academy of Sciences USA 102(15), 5397-5402. (Pubitemid 40530269)
51. EISMANN, E. R. & MÜLLER-HILL, B. (1990). Lac repressor forms stable loops in vitro with supercoiled wild-type lac DNA containing all three natural lac operators. Journal of Molecular Biology 213(4), 763-775. (Pubitemid 20213215)
52. FLATTERS, D., YOUNG, M., BEVERIDGE, D. L. & LAVERY, R. (1997). Conformational properties of the TATA-box binding sequence of DNA. Journal of Biomolecular Structure & Dynamics 14(6), 757-765. (Pubitemid 27256031)
53. FUJIMOTO, B. S. & SCHURR, J. M. (1990). Dependence of the torsional rigidity of DNA on base composition. Nature 344(6262), 175-177.
54. GARCIA, H. G., GRAYSON, P., HAN, L., INAMDAR, M., KONDEV, J., NELSON, P. C., PHILLIPS, R., WIDOM, J. & WIGGINS, P. A. (2007). Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers 85, 115-130. (Pubitemid 46306069)
55. GELBART, W.M. & KNOBLER, C. M. (2009). Virology: pressurized viruses. Science 323(5922), 1682-1683.
56. GHATAK, A. & DAS, A. L. (2007). Kink instability of a highly deformable elastic cylinder. Physical Review Letters 99(7), 076101. (Pubitemid 47267854)
57. GONDOR, A., ROUGIER, C. & OHLSSON, R. (2008). Highresolution circular chromosome conformation capture assay. Nature Protocols 3(2), 303-313. (Pubitemid 351266514)
58. GOODSELL, D. S. & DICKERSON, R. E. (1994). Bending and curvature calculations in B-DNA. Nucleic Acids Research 22, 5497-5503.
59. GOSULE, L. C. & SCHELLMAN, J. A. (1978). DNA condensation with polyamines. I. Spectroscopic studies. Journal of Molecular Biology 121, 311-326. (Pubitemid 8361801)
60. GREGORY, T. R. (2005). Genome size evolution in animals. In The Evolution of the Genome (ed. T. R. Gregory), pp. 3-87. San Diego: Elsevier.
61. GREIDER, C. W. (1999). Telomeres do D-loop-T-loop. Cell 97(4), 419-422.
62. GROMIHA, M. M. (2000). Structure based sequence dependent stiffness scale for trinucleotides: a direct method. Journal of Biological Physics 26, 43-50.
63. GROSSCHEDL, R., GIESE, K. & PAGEL, J. (1994). HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends in Genetics 10(3), 94-100. (Pubitemid 24075089)
64. GUO, Z., TAUBES, C. H., OH, J.-E., MAHER, L. J. III & MOHANTY, U. (2008). DNA on a tube: electrostatic contribution to stiffness. Journal of Physical Chemistry B 112(50), 16163-16169.
65. HAGERMAN, K. R. & HAGERMAN, P. J. (1996). Helix rigidity of DNA: the meroduplex as an experimental paradigm. Journal of Molecular Biology 260(2), 207-223.
66. HAGERMAN, P. (1990). Sequence-directed curvature of DNA. Annual Review of Biochemistry 59, 755-781. (Pubitemid 20207023)
67. HAGERMAN, P. J. (1981). Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers 20(7), 1503-1535.
68. HAGERMAN, P. J. (1985). Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry 24(25), 7033-7037.
69. HAGERMAN, P. J. (1988). Flexibility of DNA. Annual Review of Biophysics and Biophysical Chemistry 17, 265-286.
70. HAGERMAN, P. J. (1992). Straightening out the bends in curved DNA. Biochimica et Biophysica Acta 1131, 125-132.
71. HAGERMAN, P. J. & RAMADEVI, V. A. (1990). Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. I. Computational analysis. Journal of Molecular Biology 212(2), 351-362. (Pubitemid 20130733)
72. HAMELBERG, D., MCFAIL-ISOM, L., WILLIAMS, L.D. & WILSON, W. D. (2000). Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics. Journal of the American Chemical Society 122(43), 10513-10520.
73. HAMELBERG, D., WILLIAMS, L.D. & WILSON, W. D. (2001). Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequencedependent effects. Journal of the American Chemical Society 123(32), 7745-7755. (Pubitemid 32899339)
74. HAN, L., GARCIA, H. G., BLUMBERG, S., TOWLES, K. B., BEAUSANG, J. F., NELSON, P.C. & PHILLIPS, R. (2009). Concentration and length dependence of DNA looping in transcriptional regulation. PLoS ONE 4(5), e5621.
75. HARDWIDGE, P. R., PANG, Y. P., ZIMMERMAN, J. M., VAGHEFI, M., HOGREFE, R. & MAHER, L. J. (2009). Phosphate crowding and DNA bending. In Nucleic Acids: Curvature and Deformation (eds. N. C. Stellwagen and U. Mohanty), pp. 111-131. Washington, DC: American Chemical Society.
76. HARRIS, S. A. (2006). Modelling the biomechanical properties of DNA using computer simulation. Philosophical Transactions Series A, Mathematical, Physical, and Engineering Sciences 364(1849), 3319-3334. (Pubitemid 44954194)
77. HARRIS, S. A., LAUGHTON, C. A. & LIVERPOOL, T. B. (2008). Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Research 36(1), 21-29.
78. HARRIS, S. A., SANDS, Z.A. & LAUGHTON, C. A. (2005). Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophysical Journal 88(3), 1684-1691.
79. HARVEY, S. C., DLAKIC, M., GRIFFITH, J., HARRINGTON, R., PARK, K., SPROUS, D. & ZACHARIAS, W. (1995). What is the basis of sequence-directed curvature in DNAs containing A tracts ? Journal of Biomolecular Structure and Dynamics 13(2), 301-307.
80. HOCK, R., FURUSAWA, T., UEDA, T. & BUSTIN, M. (2007). HMG chromosomal proteins in development and disease. Trends in Cell Biology 17(2), 72-79. (Pubitemid 46206113)
81. HOGAN, M., LEGRANGE, J. & AUSTIN, B. (1983). Dependence of DNA helix flexibility on base composition. Nature 304(5928), 752-754. (Pubitemid 13037728)
82. HOGAN, M. E., ROONEY, T.F. & AUSTIN, R. H. (1987). Evidence for kinks in DNA folding in the nucleosome. Nature 328(6130), 554-557.
83. HOWERTON, S. B., SINES, C. C., VANDERVEER, D. & WILLIAMS, L. D. (2001). Locating monovalent cations in the grooves of B-DNA. Biochemistry 40(34), 10023-10031.
84. HUD, N. V., DOWNING, K.H. & BALHORN, R. (1995). A constant radius of curvature model for the organization of DNA in toroidal condensates. Proceedings of National Academy of Science, USA 92, 3581-3585.
85. HUD, N.V. & FEIGON, J. (1997). Localization of divalent metal ions in the minor groove of DNA A-tracts. Journal of the American Chemical Society 119(24), 5756-5757. (Pubitemid 27321444)
86. HUD, N.V. & FEIGON, J. (2002). Characterization of divalent cation localization in the minor groove of the AnTn and TnAn DNA sequence elements by 1H NMR spectroscopy and manganese(II). Biochemistry 41(31), 9900-9910.
87. HUD, N.V. & PLAVEC, J. (2003). A unified model for the origin of DNA sequence-directed curvature. Biopolymers 69(1), 144-158. (Pubitemid 36547063)
88. HUD, N. V. & POLAK, M. (2001). DNA-cation interactions: The major and minor grooves are flexible ionophores. Current Opinion in Structural Biology 11(3), 293-301. (Pubitemid 32568268)
89. HUD, N. V., SCHULTZE, P. & FEIGON, J. (1998). Ammonium ion as an NMR probe for monovalent cation coordination sites of DNA quadruplexes. Journal of the American Chemical Society 120(25), 6403-6404. (Pubitemid 28346417)
90. HUD, N. V., SKLENAR, V. & FEIGON, J. (1999). Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. Journal of Molecular Biology 286(3), 651-660. (Pubitemid 29106207)
91. JACOB, F. & MONOD, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3, 318-356.
92. JAYARAM, B., SPROUS, D., YOUNG, M.A. & BEVERIDGE, D. L. (1998). Free energy analysis of the conformational preferences of A and B forms of DNA in solution. Journal of the American Chemical Society 120(41), 10629-10633. (Pubitemid 28498806)
93. KAHN, J.D. & CROTHERS, D. M. (1992). Protein-induced bending and DNA cyclization. Proceeding of the National Academy of Sciences, USA 89, 6343-6347.
94. KAHN, J. D., YUN, E. & CROTHERS, D. M. (1994). Detection of localized DNA flexibility. Nature 368, 163-166. (Pubitemid 24101530)
95. KAPLAN, N., MOORE, I. K., FONDUFE-MITTENDORF, Y., GOSSETT, A. J., TILLO, D., FIELD, Y., LEPROUST, E. M., HUGHES, T. R., LIEB, J. D., WIDOM, J. & SEGAL, E. (2009). The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458(7236), 362-366.
96. KOO, H.-S. & CROTHERS, D. M. (1988). Calibration of DNA curvature and a unified description of sequencedirected bending. Proceedings of National Academy of Sciences, USA 85, 1763-1767.
97. KOO, H.-S., DRAK, J., RICE, J.A. & CROTHERS, D.M. (1990). Determination of the extent of DNA bending by an adenine-thymine tract. Biochemistry 29, 4227-4234. (Pubitemid 20145661)
98. KOO, H.-S., WU, H.-M. & CROTHERS, D. M. (1986). DNA bending at adenine-thymine tracts. Nature 320, 501-506.
99. KOSIKOV, K. M., GORIN, A. A., LU, X. J., OLSON, W.K. & MANNING, G. S. (2002). Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. Journal of the American Chemical Society 124(17), 4838-4847. (Pubitemid 34465023)
100. KRAMER, H., AMOUYAL, M., NORDHEIM, A. & MÜLLERHILL, B. (1988). DNA supercoiling changes the spacing requirements of two lac operators for DNA loop formation with lac repressor. EMBO Journal 7, 547-556.
101. KRAMER, H., NIEMOLLER, M., AMOUYAL, M., REVET, B., VON WILCKEN-BERGMANN, B. & MÜLLER-HILL, B. (1987). lac repressor forms loops with linear DNA carrying two suitably spaced lac operators. EMBO Journal 6(5), 1481-1491.
102. KRATKY, O. & POROD, G. (1949). Röntgenuntersuchung gelöster fadenmoleküle. Recueil des Travaux Chimiques des Pays-Bas 68, 1106-1123.
103. KRUITHOF, M., CHIEN, F. T., ROUTH, A., LOGIE, C., RHODES, D. & VAN NOORT, J. (2009). Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber. Nature Sructural and Molecular Biology 16(5), 534-540.
104. KUZNETSOV, S. V., SUGIMURA, S., VIVAS, P., CROTHERS, D. M. & ANSARI, A. (2006). Direct observation of DNA bending/unbending kinetics in complex with DNAbending protein IHF. Proceedings of the National Academy of Sciences USA 103(49), 18515-18520. (Pubitemid 44913442)
105. LANKAS, F., LAVERY, R. & MADDOCKS, J. H. (2006). Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure 14(10), 1527-1534. (Pubitemid 44486810)
106. LAW, S. M., BELLOMY, G. R., SCHLAX, P. J. & RECORD, JR., M. T. (1993). In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo. Journal of Molecular Biology 230(1), 161-173.
107. LEWIS, D. E. & ADHYA, S. (2002). In vitro repression of the gal promoters by GalR and HU depends on the proper helical phasing of the two operators. Journal of Biological Chemistry 277(4), 2498-2504. (Pubitemid 34953272)
108. LIA, G., BENSIMON, D., CROQUETTE, V., ALLEMAND, J. F., DUNLAP, D., LEWIS, D. E., ADHYA, S. & FINZI, L. (2003). Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proceedings of the National Academy of Sciences USA 100(20), 11373-11377. (Pubitemid 37205942)
109. LIEBERMAN-AIDEN, E., VAN BERKUM, N. L., WILLIAMS, L., IMAKAEV, M., RAGOCZY, T., TELLING, A., AMIT, I., LAJOIE, B. R., SABO, P. J., DORSCHNER, M. O., SANDSTROM, R., BERNSTEIN, B., BENDER, M. A., GROUDINE, M., GNIRKE, A., STAMATOYANNOPOULOS, J., MIRNY, L. A., LANDER, E.S. & DEKKER, J. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289-293.
110. LIU, Y. & BEVERIDGE, D. L. (2001). A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data. Journal of Biomolecular Structure and Dynamics 18(4), 505-526. (Pubitemid 32164727)
111. LIVERPOOL, T. B., HARRIS, S. A. & LAUGHTON, C. A. (2008). Supercoiling and denaturation of DNA loops. Physical Review Letters 100(23), 238103.
112. LOHMAN, T. M., DEHASETH, P.L. & RECORD, JR., M. T. (1980). Pentalysine-deoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic acids. Biochemistry 19(15), 3522-3530.
113. LOWARY, P. T. & WIDOM, J. (1997). Nucleosome packaging and nucleosome positioning of genomic DNA. Proceedings of the National Academy of Sciences USA 94(4), 1183-1188. (Pubitemid 27087825)
114. LOWARY, P. T. & WIDOM, J. (1998). New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology 276(1), 19-42. (Pubitemid 28085408)
115. LU, X. J. & OLSON, W. K. (2003). 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research 31(17), 5108-5121.
116. LU, Y. & STELLWAGEN, N. C. (2008). Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts. Biophysical Journal 94(5), 1719-1725.
117. LUGER, K., MADER, A. W., RICHMOND, R. K., SARGENT, D. F. & RICHMOND, T. J. (1997). Crystal structure of the nucleosome core particle at 2-8 A° resolution. Nature 389(6648), 251-260.
118. MACDONALD, D., HERBERT, K., ZHANG, X., POLOGRUTO, T. & LU, P. (2001). Solution structure of an A-tract DNA bend. Journal of Molecular Biology 306(5), 1081-1098. (Pubitemid 33030006)
119. MAHER, L. J. III (2006). DNA kinks available if needed. Structure 14(10), 1479-1480.
120. MANNING, G. S. (1978). The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quarterly Reviews of Biophysics 2, 179-246.
121. MANNING, G. S. (2006). The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophysical Journal 91(10), 3607-3616.
122. MANNING, G. S., EBRALIDSE, K. K., MIRZABEKOV, A.D. & RICH, A. (1989). An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups. Journal of Biomolecular Structure and Dynamics 6, 877-889. (Pubitemid 19117694)
123. MASTROIANNI, A. J., SIVAK, D. A., GEISSLER, P.L. & ALIVISATOS, A. P. (2009). Probing the conformational distributions of subpersistence length DNA. Biophysical Journal 97(5), 1408-1417.
124. MATERESE, C. K., SAVELYEV, A. & PAPOIAN, G. A. (2009). Counterion atmosphere and hydration patterns near anucleosome core particle. Journal of the American Chemical Society 131(41), 15005-15013.
125. MATHEW-FENN, R. S., DAS, R. & HARBURY, P. A. (2008). Remeasuring the double helix. Science 322(5900), 446-449.
126. MATSUMOTO, A. & OLSON, W. K. (2002). Sequencedependent motions of DNA: a normal mode analysis at the base-pair level. Biophysical Journal 83(1), 22-41. (Pubitemid 34694718)
127. MCCAULEY, M., HARDWIDGE, P. R., MAHER, L. J. III & WILLIAMS, M. C. (2005). Dual binding modes for an HMG domain from human HMGB2 on DNA. Biophysical Journal 89(1), 353-364. (Pubitemid 41098290)
128. MCCONNELL, K. J. & BEVERIDGE, D. L. (2000). DNA structure: Whats in charge? Journal of Molecular Biology 304(5), 803-820.
129. MCDONALD, R. J., DRAGAN, A. I., KIRK, W. R., NEFF, K. L., PRIVALOV, P.L. & MAHER, L. J. III (2007). DNA bending by charged peptides: electrophoretic and spectroscopic analyses. Biochemistry 46(9), 2306-2316.
130. MCFAIL-ISOM, L., SINES, C.C. & WILLIAMS, L. D. (1999). DNA structure: cations in charge? Current Opinion in Structural Biology 9(3), 298-304. (Pubitemid 29454496)
131. MILLS, J.B. & HAGERMAN, P. J. (2004). Origin of the intrinsic rigidity of DNA. Nucleic Acids Research 32(13), 4055-4059.
132. MILLS, J. B., VACANO, E. & HAGERMAN, P. J. (1999). Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). Journal of Molecular Biology 285(1), 245-257. (Pubitemid 29034041)
133. MORGAN, M. A., OKAMOTO, K., KAHN, J.D. & ENGLISH, D. S. (2005). Single-molecule spectroscopic determination of lac repressor-DNA loop conformation. Biophysical Journal 89(4), 2588-2596. (Pubitemid 41401047)
134. MOSSING, M.C. & RECORD, JR., M. T. (1986). Upstream operators enhance repression of the lac promoter. Science 233(4766), 889-892.
135. MOULAEI, T., MAEHIGASHI, T., LOUNTOS, G. T., KOMEDA, S., WATKINS, D., STONE, M. P., MARKY, L. A., LI, J. S., GOLD, B. & WILLIAMS, L. D. (2005). Structure of BDNA with cations tethered in the major groove. Biochemistry 44(20), 7458-7468. (Pubitemid 40695999)
136. MULLER, J., OEHLER, S. & MÜLLER-HILL, B. (1996). Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. Journal of Molecular Biology 257(1), 21-29. (Pubitemid 126353122)
137. NADEAU, J.G. & CROTHERS, D. M. (1989). Structural basis for DNA bending. Proceedings of the National Academy of Sciences USA 86, 2622-2626.
138. NAKABACHI, A., YAMASHITA, A., TOH, H., ISHIKAWA, H., DUNBAR, H. E., MORAN, N.A. & HATTORI, M. (2006). The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314(5797), 267. (Pubitemid 44571965)
139. NGUYEN, T.T. & SHKLOVSKII, B. I. (2002). Persistence length of a polyelectrolyte in salty water: Monte Carlo study. Physical Reviews E, Statistical, Nonlinear, and Soft Matter Physics 66(2 Pt 1), 021801.
140. NOOTHI, S. K., KOMBRABAIL, M., KUNDU, T. K., KRISHNAMOORTHY, G. & RAO, B. J. (2009). Enhanced DNA dynamics due to cationic reagents, topological states of dsDNA and high mobility group box 1 as probed by PicoGreen. FEBS Journal 276(2), 541-551.
141. OEHLER, S., EISMANN, E. R., KRAMER, H. & MÜLLER-HILL, B. (1990). The three operators of the lac operon cooperate in repression. EMBO Journal 9(4), 973-979. (Pubitemid 20110557)
142. OEHLER, S. & MÜLLER-HILL, B. (2009). High local concentration: a fundamental strategy of life. Journal of Molecular Biology 395(2), 242-253.
143. OKONOGI, T. M., ALLEY, S. C., HARWOOD, E. A., HOPKINS, P. B. & ROBINSON, B. H. (2002). Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding. Proceedings of National Academy of Science USA 99, 4156-4160.
144. OKONOGI, T. M., REESE, A. W., ALLEY, S. C., HOPKINS, P. B. & ROBINSON, B. H. (1999). Flexibility of duplex DNA on the submicrosecond timescale. Biophysical Journal 77(6), 3256-3276.
145. OLSON, W. K., GORIN, A. A., LU, X. J., HOCK, L.M. & ZHURKIN, V. B. (1998). DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences USA 95(19), 11163-11168.
146. OLSON, W. K., SWIGON, D. & COLEMAN, B. D. (2004). Implications of the dependence of the elastic properties of DNA on nucleotide sequence. Philosophical Transactions Series A, Mathematical, Physical, and Engineering Sciences 362(1820), 1403-1422. (Pubitemid 38846199)
147. OLSON, W.K. & ZHURKIN, V. B. (2000). Modeling DNA deformations. Current Opinion in Structural Biology 10(3), 286-297.
148. PARKER, S. C., HANSEN, L., ABAAN, H. O., TULLIUS, T. D. & MARGULIES, E. H. (2009). Local DNA topography correlates with functional noncoding regions of the human genome. Science 324(5925), 389-392.
149. PAULL, T. T., CAREY, M. & JOHNSON, R. C. (1996). Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. Genes and Development 10, 2769-2781. (Pubitemid 26384496)
150. PAULL, T. T., HAYKINSON, M. J. & JOHNSON, R. C. (1993). The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes and Development 7(8), 1521-1534.
151. PAULL, T. T. & JOHNSON, R. C. (1995). DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B. Journal of Biological Chemistry 270, 8744-8754.
152. PODESTA, A., IMPERADORI, L., COLNAGHI, W., FINZI, L., MILANI, P. & DUNLAP, D. (2004). Atomic force microscopy study of DNA deposited on poly L-ornithine-coated mica. Journal of Microscopy 215(Pt 3), 236-240. (Pubitemid 39233711)
153. PODESTA, A., INDRIERI, M., BROGIOLI, D., MANNING, G. S., MILANI, P., GUERRA, R., FINZI, L. & DUNLAP, D. (2005). Positively charged surfaces increase the flexibility of DNA. Biophysical Journal 89(4), 2558-2563. (Pubitemid 41401044)
154. PODTELEZHNIKOV, A. A., MAO, C., SEEMAN, N.C. & VOLOGODSKII, A. (2000). Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophysical Journal 79(5), 2692-2704.
155. POPOV, Y.O. & TKACHENKO, A. V. (2005). Effects of kinks on DNA elasticity. Physical Reviews E, Statistics, Nonlinear, and Soft Matter Physics 71(5 Pt 1), 051905.
156. PROTOZANOVA, E., YAKOVCHUK, P. & FRANK-KAMENETSKII, M. D. (2004). Stacked-unstacked equilibrium at the nick site of DNA. Journal of Molecular Biology 342(3), 775-785. (Pubitemid 39165649)
157. PTASHNE, M. & GANN, A. (1997). Transcriptional activation by recruitment. Nature 386(6625), 569-577. (Pubitemid 27175417)
158. RANDALL, G. L., ZECHIEDRICH, L. & PETTITT, B. M. (2009). In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form. Nucleic Acids Research 37, 5568-5577.
159. RANGE, K., MAYAAN, E., MAHER, L. J. III & YORK, D.M. (2005). The contribution of phosphate-phosphate repulsions to the free energy of DNA bending. Nucleic Acids Research 33(4), 1257-1268. (Pubitemid 41439919)
160. RANGEL, D. P., FUJIMOTO, B. S. & SCHURR, J. M. (2008). Estimation of the persistence length of DNA from the torsion elastic constant and supercoiling free energy: effect of ethylene glycol. Journal of Physical Chemistry B 112(42), 13359-13366.
161. RECORD, JR., M. T., ANDERSON, C.F. & LOHMAN, T.M. (1978). Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Quarterly Reviews of Biophysics 11(2), 103-178.
162. RECORD, JR., M. T., DEHASETH, P.L. & LOHMAN, T.M. (1977). Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. Biochemistry 16(22), 4791-4796. (Pubitemid 8220967)
163. RICHMOND, T. J. & DAVEY, C. A. (2003). The structure of DNA in the nucleosome core. Nature 423(6936), 145-150.
164. RINGROSE, L., CHABANIS, S., ANGRAND, P. O., WOODROOFE, C. & STEWART, A. F. (1999). Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances. EMBO Journal 18(23), 6630-6641.
165. RIPPE, K. (2001). Making contacts on a nucleic acid polymer. Trends in Biochemical Science 26(12), 733-740. (Pubitemid 34014840)
166. RIPPE, K., VON HIPPEL, P.H. & LANGOWSKI, J. (1995). Action at a distance: DNA-looping and initiation of transcription. Trends is Biochemical Science 20(12), 500-506.
167. ROHS, R.,WEST, S. M., SOSINSKY, A., LIU, P., MANN, R. S. & HONIG, B. (2009). The role of DNA shape in protein- DNA recognition. Nature 461(7268), 1248-1253.
168. ROSS, E. D., DEN, R. B., HARDWIDGE, P. R. & MAHER, L. J. III (1999). Improved quantitation of DNA curvature using ligation ladders. Nucleic Acids Research 27(21), 4135-4142.
169. ROSS, E. D., HARDWIDGE, P. R. & MAHER, L. J. III (2001). HMG proteins and DNA flexibility in transcription activation. Molecular and Cellular Biology 21(19), 6598-6605.
170. ROTHEMUND, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440(7082), 297-302.
171. ROUZINA, I. & BLOOMFIELD, V. A. (1998). DNA bending by small, mobile multivalent cations. Biophysical Journal 74(6), 3152-3164.
172. ROUZINA, I. & BLOOMFIELD, V. A. (2001a). Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophysical Journal 80(2), 882-893. (Pubitemid 32128339)
173. ROUZINA, I. & BLOOMFIELD, V. A. (2001b). Force-induced melting of the DNA double helix. 2. Effect of solution conditions. Biophysical Journal 80(2), 894-900. (Pubitemid 32128340)
174. ROYCHOUDHURY, M., SITLANI, A., LAPHAM, J. & CROTHERS, D. M. (2000). Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proceedings of the National Academy of Sciences USA 97(25), 13608-13613.
175. SANTALUCIA, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences USA 95(4), 1460-1465. (Pubitemid 28103414)
176. SATCHWELL, S. C., DREW, H. R. & TRAVERS, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology 191(4), 659-675. (Pubitemid 17185964)
177. SCHULTZ, S. C., SHIELDS, G.C. & STEITZ, T. A. (1991). Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253(5023), 1001-1007.
178. SCHURR, J. M. (2009). Polyanion Models of Nucleic Acid- Metal Ion Interactions. In Nucleic Acid-Metal Ion Interactions (ed. N. V. Hud), pp. 307-349. Cambridge: RSC.
179. SCHURR, J.M. & ALLISON, S. A. (1981). Polyelectrolyte contribution to the persistence length of DNA. Biopolymers 20(2), 251-268.
180. SCHURR, J.M. & FUJIMOTO, B. S. (2002). Extensions of counterion condensation theory. I. Alternative geometries and finite salt concentration. Biophysical Chemistry 101-102, 425-445.
181. SCIPIONI, A., ANSELMI, C., ZUCCHERI, G., SAMORI, B. & DE SANTIS, P. (2002a). Sequence-dependent DNA curvature and flexibility from scanning force microscopy images. Biophysical Journal 83(5), 2408-2418. (Pubitemid 35265737)
182. SCIPIONI, A., ZUCCHERI, G., ANSELMI, C., BERGIA, A., SAMORI, B. & DE SANTIS, P. (2002b). Sequencedependent DNA dynamics by scanning force microscopy time-resolved imaging. Chemistry and Biology 9(12), 1315-1321. (Pubitemid 36010687)
183. SEBASTIAN, N. T., BYSTRY, E. M., BECKER, N. A. & MAHER, L. J. III (2009). Enhancement of DNA flexibility in vitro and in vivo by HMGB box A proteins carrying box B residues. Biochemistry 48(10), 2125-2134.
184. SEEMAN, N. C. (2006). DNA enables nanoscale control of the structure of matter. Quarterly Reviews of Biophysics 38, 363-371.
185. SEGAL, E., FONDUFE-MITTENDORF, Y., CHEN, L., THASTROM, A., FIELD, Y., MOORE, I. K., WANG, J. P. & WIDOM, J. (2006). A genomic code for nucleosome positioning. Nature 442(7104), 772-778. (Pubitemid 44258903)
186. SELSING, E., WELLS, R. D., ALDEN, C. J. & ARNOTT, S. (1979). Bent DNA: visualization of a base-paired and stacked A-B conformational junction. Journal of Biological Chemistry 254(12), 5417-5422. (Pubitemid 9231905)
187. SERGEYEV, V., PYSHKINA, O., LEZOV, A., MELNIKOV, A., RYUMTSEV, E., ZEZIN, A. & KABANOV, V. (1999). DNA complexed with oppositely charged amphiphile in lowpolar organic solvents. Langmuir 15, 4435-4444.
188. SHIMADA, J. & YAMAKAWA, H. (1984). Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17, 689-698.
189. SHORE, D. & BALDWIN, R. L. (1983). Energetics of DNA twisting. I. Relation between twist and cyclization probability. Journal of Molecular Biology 170, 957-981. (Pubitemid 14249345)
190. SHORE, D., LANGOWSKI, J. & BALDWIN, R. L. (1981). DNA flexibility studied by covalent closure of short fragments into circles. Proceedings of the National Academy of Sciences USA 78(8), 4833-4837. (Pubitemid 12225575)
191. SHUI, X., MCFAIL-ISOM, L., HU, G.G. & WILLIAMS, L.D. (1998a). The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37, 8341-8355. (Pubitemid 28275453)
192. SHUI, X., SINES, C., MCFAIL-ISOM, L., VANDERVEER, D. & WILLIAMS, L. D. (1998b). Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry 37, 16877-16887. (Pubitemid 28566764)
193. SINES, C. C., MCFAIL-ISOM, L., HOWERTON, S. B., VANDERVEER, D. & WILLIAMS, L. D. (2000). Cations mediate B-DNA conformational heterogeneity. Journal of the American Chemical Society 122(45), 11048-11056.
194. SIVOLOB, A. V. & KHRAPUNOV, S. N. (1995). Translational positioning of nucleosomes on DNA: The role of sequence-dependent isotropic DNA bending stiffness. Journal of Molecular Biology 247, 918-931.
195. SKOLNICK, J. & FIXMAN, M. (1977). Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules 10, 944-948.
196. SPROUS, D., YOUNG, M.A. & BEVERIDGE, D. L. (1998). Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/ water mixture: Theoretical considerations of the A-B transition. Journal of Physical Chemistry 102(23), 4658-4667. (Pubitemid 128578331)
197. STELLWAGEN, N. C., MAGNUSDOTTIR, S., GELFI, C. & RIGHETTI, P. G. (2001). Preferential counterion binding to A-tract DNA oligomers. Journal of Molecular Biology 305(5), 1025-1033. (Pubitemid 33027740)
198. STRAUSS, J. K. & MAHER, L. J. III (1994). DNA bending by asymmetric phosphate neutralization. Science 266(5192), 1829-1834.
199. SWIGON, D., COLEMAN, B.D. & OLSON, W. K. (2006). Modeling the lac repressor-operator assembly: the influence of DNA looping on lac repressor conformation. Proceedings of the National Academy of Sciences USA 103(26), 9879-9884. (Pubitemid 43993591)
200. TAYLOR, W.H. & HAGERMAN, P. J. (1990). Application of the method of phage T4 DNA ligase-catalyzed ringclosure to the study of DNA structure. II. NaCldependence of DNA flexibility and helical repeat. Journal of Molecular Biology 212(2), 363-376. (Pubitemid 20130734)
201. THOMAS, J.O. & TRAVERS, A. A. (2001). HMG1 and 2, and related architectural DNA-binding proteins. Trends in Biochemical Science 26(3), 167-174. (Pubitemid 32197576)
202. TINOCO, JR., I., LI, P.T. & BUSTAMANTE, C. (2006). Determination of thermodynamics and kinetics of RNA reactions by force. Quarterly Reviews of Biophysics 39(4), 325-360. (Pubitemid 44950379)
203. TJIAN, R. & MANIATIS, T. (1994). Transcriptional activation: a complex puzzle with few easy pieces. Cell 77, 5-8. (Pubitemid 24184680)
204. TOLHUIS, B., PALSTRA, R. J., SPLINTER, E., GROSVELD, F. & DE LAAT, W. (2002). Looping and interaction between hypersensitive sites in the active beta-globin locus. Molecular Cell 10(6), 1453-1465. (Pubitemid 36050885)
205. TRAVERS, A. A., NER, S. S. & CHURCHILL, M. E. A. (1994). DNA chaperones: a solution to a persistence problem. Cell 77, 167-169.
206. TRIFONOV, E.N. & SUSSMAN, J. L. (1980). The pitch of chromatin DNA is reflected in its nucleotide sequence. Proceedings of the National Academy of Sciences USA 77(7), 3816-3820.
207. VACANO, E. & HAGERMAN, P. J. (1997). Analysis of birefringence decay profiles for nucleic acid helices possessing bends: the tau-ratio approach. Biophysical Journal 73(1), 306-317. (Pubitemid 27274128)
208. VAN NOORT, J., VERBRUGGE, S., GOOSEN, N., DEKKER, C. & DAME, R. T. (2004). Dual architectural roles of HU: Formation of flexible hinges and rigid filaments. Proceedings of the National Academy of Sciences USA 101(18), 6969-6974. (Pubitemid 38596427)
209. VERNIMMEN, D., DE GOBBI, M., SLOANE-STANLEY, J. A., WOOD, W.G. & HIGGS, D. R. (2007). Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO Journal 26(8), 2041-2051. (Pubitemid 46625789)
210. VILLA, E., BALAEFF, A. & SCHULTEN, K. (2005). Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proceedings of the National Academy of Sciences USA 102(19), 6783-6788. (Pubitemid 40675393)
211. VIRSTEDT, J., BERGE, T., HENDERSON, R. M., WARING, M. J. & TRAVERS, A. A. (2004). The influence of DNA stiffness upon nucleosome formation. Journal of Structural Biology 148(1), 66-85. (Pubitemid 39195294)
212. VOLOGODSKAIA, M. & VOLOGODSKII, A. (2002). Contribution of the intrinsic curvature to measured DNA persistence length. Journal of Molecular Biology 317(2), 205-213. (Pubitemid 34722188)
213. WIDOM, J. (2001). Role of DNA sequence in nucleosome stability and dynamics. Quarterly Reviews of Biophysics 34(3), 269-324. (Pubitemid 34121497)
214. WIGGINS, P. A., PHILLIPS, R. & NELSON, P. C. (2005). Exact theory of kinkable elastic polymers. Physical Review E, Statistics, Nonlinear and Soft Matter Physics 71(2 Pt 1), 021909. (Pubitemid 40618357)
215. WIGGINS, P. A., VAN DER HEIJDEN, T., MORENO-HERRERO, F., SPAKOWITZ, A., PHILLIPS, R., WIDOM, J., DEKKER, C. & NELSON, P. C. (2006). High flexibility of DNA on short length scales probed by atomic force microscopy. Nature Nanotechnology 1, 137-141.
216. WILLIAMS, L.D. & MAHER, L. J. III (2000). Electrostatic mechanisms of DNA deformation. Annual Reviews of Biophysics and Biomolecular Structure 29, 497-521.
217. WILLIAMS, S. L., PARKHURST, L.K. & PARKHURST, L. J. (2006). Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer. Nucleic Acids Research 34(3), 1028-1035.
218. WITZ, G., RECHENDORFF, K., ADAMCIK, J. & DIETLER, G. (2008). Conformation of circular DNA in two dimensions. Physical Review Letters 101(14), 148103.
219. WONG, O. K., GUTHOLD, M., ERIE, D.A. & GELLES, J. (2008). Interconvertible lac repressor-DNA loops revealed by single-molecule experiments. PLoS Biology 6(9), e232.
220. WU, H.-M. & CROTHERS, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509-513.
221. YAN, J. & MARKO, J. F. (2004). Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Physical Review Letters 93(10), 108108.
222. YOUNG, M.A. & BEVERIDGE, D. L. (1998). Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. Journal of Molecular Biology 281(4), 675-687.
223. YOUNG, M. A., JAYARAM, B. & BEVERIDGE, D. L. (1997a). Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. Journal of the American Chemical Society 119, 59-69. (Pubitemid 27064483)
224. YOUNG, M. A., RAVISHANKER, G. & BEVERIDGE, D.L. (1997b). A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. Biophysical Journal 73(5), 2313-2336. (Pubitemid 27471443)
225. YOUNG, M. A., RAVISHANKER, G., BEVERIDGE, D.L. & BERMAN, H. M. (1995). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNAprotein complexes. Biophysical Journal 68(6), 2454-2468.
226. ZELLER, R. W., GRIFFITH, J. D., MOORE, J. G., KIRCHHAMER, C. V., BRITTEN, R. J. & DAVIDSON, E.H. (1995). A multimerizing transcription factor of sea urchin embryos capable of looping DNA. Proceedings of the National Academy of Sciences USA 92(7), 2989-2993.
227. ZHANG, Y. & CROTHERS, D. M. (2003). High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proceedings of the National Academy of Sciences USA 100(6), 3161-3166. (Pubitemid 36356556)
228. ZHANG, Y., MCEWEN, A. E., CROTHERS, D.M. & LEVENE, S. D. (2006a). Analysis of in-vivo LacRmediated gene repression based on the mechanics of DNA looping. PLoS ONE 1, e136.
229. ZHANG, Y., MCEWEN, A. E., CROTHERS, D.M. & LEVENE, S. D. (2006b). Statistical-mechanical theory of DNA looping. Biophysical Journal 90(6), 1903-1912.
230. ZHENG, G., LU, X. J. & OLSON, W. K. (2009). Web 3DNA-a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Research 37, W240-246.
231. ZHOU, G. L., XIN, L., SONG, W., DI, L. J., LIU, G., WU, X. S., LIU, D.P. & LIANG, C. C. (2006). Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Molecular and Cellular Biology 26(13), 5096-5105. (Pubitemid 43955822)
232. ZINKEL, S.S. & CROTHERS, D. M. (1987). DNA bend direction by phase sensitive detection. Nature 328, 178-181.