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DNA curvature and flexibility in vitro and in vivo

Published online by Cambridge University Press:  18 May 2010

Justin P. Peters  and
L. James Maher III
Justin P. Peters
Affiliation:
Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
L. James Maher III*
Affiliation:
Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
*
*Author for correspondence: Professor L. J. Maher, III, Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN55905, USA. Tel.: 507-285-9041, Fax: 507-284-2053; Email: [email protected]
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Abstract

It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent ‘softening’ of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 43 , Issue 1 , February 2010 , pp. 23 - 63
Copyright
Copyright © Cambridge University Press 2010

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References

Aki, T. & Adhya, S. (1997). Repressor induced site-specific binding of HU for transcriptional regulation. EMBO Journal 16(12), 3666–3674.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Ansari, A. & Hampsey, M. (2005). A role for the CPF 3′-end processing machinery in RNAP II-dependent gene looping. Genes and Development 19(24), 2969–2978.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Balaeff, A., Mahadevan, L. & Schulten, K. (2004). Structural basis for cooperative DNA binding by CAP and lac repressor. Structure 12(1), 123–132.CrossRefGoogle ScholarPubMed
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.Google ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.Google ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Bennett, M. D. & Leitch, I. J. (2005). Genome size evolution in plants. In The Evolution of the Genome (ed. Gregory, T. R.), pp. 89–162. San Diego: Elsevier.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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. Leontis, N. B. and Santa Lucia, J.), pp. 260–284. Washington, DC: American Chemical Society.Google Scholar
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.CrossRefGoogle ScholarPubMed
Bianchi, M. E. (1994). Prokaryotic HU and eukaryotic HMG1: a kinked relationship. Molecular Microbiology 14(1), 1–5.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Bloomfield, V. A. (1997). DNA condensation by multivalent cations. Biopolymers 44(3), 269–282.3.0.CO;2-T>CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.Google ScholarPubMed
Buratowski, S. (1994). The basics of basal transcription by RNA polymerase II. Cell 77, 1–3.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Bustin, M. (2001). Revised nomenclature for high mobility group (HMG) chromosomal proteins. Trends in Biochemical Science 26(3), 152–153.Google ScholarPubMed
Cacchione, S., De Santis, P., Foti, D., Palleschi, A. & Savino, M. (1989). Periodical polydeoxynucleotides and DNA curvature. Biochemistry 28(22), 8706–8713.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Cantor, C. & Schimmel, P. (1980). Biophysical Chemistry Part III: The Behavior of Biological Macromolecules. New York: W. H. Freeman.Google Scholar
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.CrossRefGoogle ScholarPubMed
Cloutier, T. E. & Widom, J. (2004). Spontaneous sharp bending of double-stranded DNA. Molecular Cell 14(3), 355–362.CrossRefGoogle ScholarPubMed
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.Google ScholarPubMed
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.Google ScholarPubMed
Cohen, A. E. & Moerner, W. E. (2005). Method for trapping and manipulating nanoscale objects in solution. Applied Physics Letters 86(9), 093109.CrossRefGoogle Scholar
Crick, F. H. & Klug, A. (1975). Kinky helix. Nature 255(5509), 530–533.CrossRefGoogle ScholarPubMed
Crothers, D. M. (1993). Architectural elements in nucleoprotein complexes. Current Biology 3(10), 675–676.CrossRefGoogle ScholarPubMed
Crothers, D. M. & Drak, J. (1992). Global features of DNA structure by comparative gel electrophoresis. Methods in Enzymology 212, 46–71.CrossRefGoogle ScholarPubMed
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.Google ScholarPubMed
Crothers, D. M., Haran, T. E. & Nadeau, J. G. (1990). Intrinsically bent DNA. Journal of Biological Chemistry 265, 7093–7096.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Czapla, L., Swigon, D. & Olson, W. K. (2006). Sequence-dependent effects in the cyclization of short DNA. Journal of Chemical Theory and Computation 2(3), 685–695.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
deHaseth, P. L., Lohman, T. M. & Record, M. T. Jr. (1977). Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release. Biochemistry 16(22), 4783–4790.CrossRefGoogle ScholarPubMed
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. (2002). Capturing chromosome conformation. Science 295(5558), 1306–1311.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Dobi, K. C. & Winston, F. (2007). Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Molecular and Cellular Biology 27(15), 5575–5586.CrossRefGoogle Scholar
Dong, Q., Stellwagen, E. & Stellwagen, N. C. (2009). Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry 48(5), 1047–1055.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Drew, H. R. & Travers, A. A. (1985). DNA bending and its relation to nucleosome positioning. Journal of Molecular Biology 186, 773–790.Google ScholarPubMed
Du, Q., Kotlyar, A. & Vologodskii, A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Research 36(4), 1120–1128.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Fujimoto, B. S. & Schurr, J. M. (1990). Dependence of the torsional rigidity of DNA on base composition. Nature 344(6262), 175–177.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Gelbart, W. M. & Knobler, C. M. (2009). Virology: pressurized viruses. Science 323(5922), 1682–1683.CrossRefGoogle ScholarPubMed
Ghatak, A. & Das, A. L. (2007). Kink instability of a highly deformable elastic cylinder. Physical Review Letters 99(7), 076101.CrossRefGoogle ScholarPubMed
Gondor, A., Rougier, C. & Ohlsson, R. (2008). High-resolution circular chromosome conformation capture assay. Nature Protocols 3(2), 303–313.Google ScholarPubMed
Goodsell, D. S. & Dickerson, R. E. (1994). Bending and curvature calculations in B-DNA. Nucleic Acids Research 22, 5497–5503.CrossRefGoogle ScholarPubMed
Gosule, L. C. & Schellman, J. A. (1978). DNA condensation with polyamines. I. Spectroscopic studies. Journal of Molecular Biology 121, 311–326.CrossRefGoogle ScholarPubMed
Gregory, T. R. (2005). Genome size evolution in animals. In The Evolution of the Genome (ed. Gregory, T. R.), pp. 3–87. San Diego: Elsevier.CrossRefGoogle Scholar
Greider, C. W. (1999). Telomeres do D-loop-T-loop. Cell 97(4), 419–422.CrossRefGoogle ScholarPubMed
Gromiha, M. M. (2000). Structure based sequence dependent stiffness scale for trinucleotides: a direct method. Journal of Biological Physics 26, 43–50.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Hagerman, P. (1990). Sequence-directed curvature of DNA. Annual Review of Biochemistry 59, 755–781.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1981). Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers 20(7), 1503–1535.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1985). Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry 24(25), 7033–7037.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1988). Flexibility of DNA. Annual Review of Biophysics and Biophysical Chemistry 17, 265–286.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1992). Straightening out the bends in curved DNA. Biochimica et Biophysica Acta 1131, 125–132.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Hamelberg, D., Williams, L. D. & Wilson, W. D. (2001). Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects. Journal of the American Chemical Society 123(32), 7745–7755.CrossRefGoogle ScholarPubMed
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.Google ScholarPubMed
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. Stellwagen, N. C. and Mohanty, U.), pp. 111–131. Washington, DC: American Chemical Society.Google Scholar
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.Google ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Hock, R., Furusawa, T., Ueda, T. & Bustin, M. (2007). HMG chromosomal proteins in development and disease. Trends in Cell Biology 17(2), 72–79.CrossRefGoogle ScholarPubMed
Hogan, M., Legrange, J. & Austin, B. (1983). Dependence of DNA helix flexibility on base composition. Nature 304(5928), 752–754.CrossRefGoogle ScholarPubMed
Hogan, M. E., Rooney, T. F. & Austin, R. H. (1987). Evidence for kinks in DNA folding in the nucleosome. Nature 328(6130), 554–557.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Hud, N. V. & Plavec, J. (2003). A unified model for the origin of DNA sequence-directed curvature. Biopolymers 69(1), 144–158.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Jacob, F. & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3, 318–356.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Kahn, J. D. & Crothers, D. M. (1992). Protein-induced bending and DNA cyclization. Proceeding of the National Academy of Sciences, USA 89, 6343–6347.CrossRefGoogle ScholarPubMed
Kahn, J. D., Yun, E. & Crothers, D. M. (1994). Detection of localized DNA flexibility. Nature 368, 163–166.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Koo, H.-S. & Crothers, D. M. (1988). Calibration of DNA curvature and a unified description of sequence-directed bending. Proceedings of National Academy of Sciences, USA 85, 1763–1767.Google Scholar
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.CrossRefGoogle ScholarPubMed
Koo, H.-S., Wu, H.-M. & Crothers, D. M. (1986). DNA bending at adenine-thymine tracts. Nature 320, 501–506.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Kramer, H., Amouyal, M., Nordheim, A. & Müller-Hill, B. (1988). DNA supercoiling changes the spacing requirements of two lac operators for DNA loop formation with lac repressor. EMBO Journal 7, 547–556.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Kratky, O. & Porod, G. (1949). Röntgenuntersuchung gelöster fadenmoleküle. Recueil des Travaux Chimiques des Pays-Bas 68, 1106–1123.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Kuznetsov, S. V., Sugimura, S., Vivas, P., Crothers, D. M. & Ansari, A. (2006). Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF. Proceedings of the National Academy of Sciences USA 103(49), 18515–18520.CrossRefGoogle ScholarPubMed
Lankas, F., Lavery, R. & Maddocks, J. H. (2006). Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure 14(10), 1527–1534.CrossRefGoogle ScholarPubMed
Law, S. M., Bellomy, G. R., Schlax, P. J. & Record, M. T. Jr. ( 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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.Google ScholarPubMed
Liverpool, T. B., Harris, S. A. & Laughton, C. A. (2008). Supercoiling and denaturation of DNA loops. Physical Review Letters 100(23), 238103.CrossRefGoogle ScholarPubMed
Lohman, T. M., Dehaseth, P. L. & Record, M. T. Jr. ( 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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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 Å resolution. Nature 389(6648), 251–260.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Maher, L. J. III (2006). DNA kinks available … if needed. Structure 14(10), 1479–1480.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Materese, C. K., Savelyev, A. & Papoian, G. A. (2009). Counterion atmosphere and hydration patterns near a nucleosome core particle. Journal of the American Chemical Society 131(41), 15005–15013.CrossRefGoogle Scholar
Mathew-Fenn, R. S., Das, R. & Harbury, P. A. (2008). Remeasuring the double helix. Science 322(5900), 446–449.CrossRefGoogle ScholarPubMed
Matsumoto, A. & Olson, W. K. (2002). Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level. Biophysical Journal 83(1), 22–41.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Mcconnell, K. J. & Beveridge, D. L. (2000). DNA structure: What's in charge? Journal of Molecular Biology 304(5), 803–820.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Mcfail-Isom, L., Sines, C. C. & Williams, L. D. (1999). DNA structure: cations in charge? Current Opinion in Structural Biology 9(3), 298–304.CrossRefGoogle ScholarPubMed
Mills, J. B. & Hagerman, P. J. (2004). Origin of the intrinsic rigidity of DNA. Nucleic Acids Research 32(13), 4055–4059.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Mossing, M. C. & Record, M. T. Jr. (1986). Upstream operators enhance repression of the lac promoter. Science 233(4766), 889–892.CrossRefGoogle ScholarPubMed
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 B-DNA with cations tethered in the major groove. Biochemistry 44(20), 7458–7468.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Nadeau, J. G. & Crothers, D. M. (1989). Structural basis for DNA bending. Proceedings of the National Academy of Sciences USA 86, 2622–2626.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Oehler, S. & Müller-Hill, B. (2009). High local concentration: a fundamental strategy of life. Journal of Molecular Biology 395(2), 242–253.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Olson, W. K. & Zhurkin, V. B. (2000). Modeling DNA deformations. Current Opinion in Structural Biology 10(3), 286–297.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Ptashne, M. & Gann, A. (1997). Transcriptional activation by recruitment. Nature 386(6625), 569–577.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Record, M. T. Jr., 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.CrossRefGoogle ScholarPubMed
Record, M. T. Jr., 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.CrossRefGoogle ScholarPubMed
Richmond, T. J. & Davey, C. A. (2003). The structure of DNA in the nucleosome core. Nature 423(6936), 145–150.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Rippe, K. (2001). Making contacts on a nucleic acid polymer. Trends in Biochemical Science 26(12), 733–740.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Rothemund, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440(7082), 297–302.CrossRefGoogle ScholarPubMed
Rouzina, I. & Bloomfield, V. A. (1998). DNA bending by small, mobile multivalent cations. Biophysical Journal 74(6), 3152–3164.CrossRefGoogle ScholarPubMed
Rouzina, I. & Bloomfield, V. A. (2001a). Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophysical Journal 80(2), 882–893.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Schurr, J. M. (2009). Polyanion Models of Nucleic Acid-Metal Ion Interactions. In Nucleic Acid–Metal Ion Interactions (ed. Hud, N. V.), pp. 307–349. Cambridge: RSC.Google Scholar
Schurr, J. M. & Allison, S. A. (1981). Polyelectrolyte contribution to the persistence length of DNA. Biopolymers 20(2), 251–268.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Scipioni, A., Zuccheri, G., Anselmi, C., Bergia, A., Samori, B. & De Santis, P. (2002b). Sequence-dependent DNA dynamics by scanning force microscopy time-resolved imaging. Chemistry and Biology 9(12), 1315–1321.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Seeman, N. C. (2006). DNA enables nanoscale control of the structure of matter. Quarterly Reviews of Biophysics 38, 363–371.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Sergeyev, V., Pyshkina, O., Lezov, A., Mel'nikov, A., Ryumtsev, E., Zezin, A. & Kabanov, V. (1999). DNA complexed with oppositely charged amphiphile in low-polar organic solvents. Langmuir 15, 4435–4444.CrossRefGoogle Scholar
Shimada, J. & Yamakawa, H. (1984). Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17, 689–698.CrossRefGoogle Scholar
Shore, D. & Baldwin, R. L. (1983). Energetics of DNA twisting. I. Relation between twist and cyclization probability. Journal of Molecular Biology 170, 957–981.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Skolnick, J. & Fixman, M. (1977). Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules 10, 944–948.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Strauss, J. K. & Maher, L. J. III ( 1994). DNA bending by asymmetric phosphate neutralization. Science 266(5192), 1829–1834.Google ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Taylor, W. H. & Hagerman, P. J. (1990). Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. Journal of Molecular Biology 212(2), 363–376.CrossRefGoogle Scholar
Thomas, J. O. & Travers, A. A. (2001). HMG1 and 2, and related ‘architectural’ DNA-binding proteins. Trends in Biochemical Science 26(3), 167–174.CrossRefGoogle ScholarPubMed
Tinoco, I. Jr., Li, P. T. & Bustamante, C. (2006). Determination of thermodynamics and kinetics of RNA reactions by force. Quarterly Reviews of Biophysics 39(4), 325–360.CrossRefGoogle ScholarPubMed
Tjian, R. & Maniatis, T. (1994). Transcriptional activation: a complex puzzle with few easy pieces. Cell 77, 5–8.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Travers, A. A., Ner, S. S. & Churchill, M. E. A. (1994). DNA chaperones: a solution to a persistence problem. Cell 77, 167–169.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.Google ScholarPubMed
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.Google ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Vologodskaia, M. & Vologodskii, A. (2002). Contribution of the intrinsic curvature to measured DNA persistence length. Journal of Molecular Biology 317(2), 205–213.CrossRefGoogle ScholarPubMed
Widom, J. (2001). Role of DNA sequence in nucleosome stability and dynamics. Quarterly Reviews of Biophysics 34(3), 269–324.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Williams, L. D. & Maher, L. J. III ( 2000). Electrostatic mechanisms of DNA deformation. Annual Reviews of Biophysics and Biomolecular Structure 29, 497–521.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Witz, G., Rechendorff, K., Adamcik, J. & Dietler, G. (2008). Conformation of circular DNA in two dimensions. Physical Review Letters 101(14), 148103.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Wu, H.-M. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509–513.CrossRefGoogle ScholarPubMed
Yan, J. & Marko, J. F. (2004). Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Physical Review Letters 93(10), 108108.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Young, M. A., Ravishanker, G., Beveridge, D. L. & Berman, H. M. (1995). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophysical Journal 68(6), 2454–2468.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Zhang, Y., Mcewen, A. E., Crothers, D. M. & Levene, S. D. (2006a). Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. PLoS ONE 1, e136.CrossRefGoogle ScholarPubMed
Zhang, Y., Mcewen, A. E., Crothers, D. M. & Levene, S. D. (2006b). Statistical-mechanical theory of DNA looping. Biophysical Journal 90(6), 1903–1912.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Zinkel, S. S. & Crothers, D. M. (1987). DNA bend direction by phase sensitive detection. Nature 328, 178–181.CrossRefGoogle ScholarPubMed