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Bullied no more: when and how DNA shoves proteins around

Published online by Cambridge University Press:  31 July 2012

Jonathan M. Fogg ,
Graham L. Randall ,
B. Montgomery Pettitt ,
De Witt L. Sumners ,
Sarah A. Harris  and
Lynn Zechiedrich
Jonathan M. Fogg
Affiliation:
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA
Graham L. Randall
Affiliation:
Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030-3411, USA Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA
B. Montgomery Pettitt
Affiliation:
Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030-3411, USA Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA
De Witt L. Sumners
Affiliation:
Department of Mathematics, Florida State University, Tallahassee, FL 32306-4510, USA
Sarah A. Harris
Affiliation:
School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
Lynn Zechiedrich*
Affiliation:
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030-3411, USA
*
†Author for correspondence: Lynn Zechiedrich, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA. Tel.: 1 (713) 798-5126; Fax: 1 (713) 798-7375; Email: [email protected]
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Abstract

The predominant protein-centric perspective in protein–DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 45 , Issue 3 , August 2012 , pp. 257 - 299
Copyright
Copyright © Cambridge University Press 2012

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References

Aggarwal, A., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. (1988). Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242, 899–907.CrossRefGoogle ScholarPubMed
Ahmad, S., Kono, H., Araúzo-Bravo, M. J. & Sarai, A. (2006). Readout: structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition. Nucleic Acids Research 34, W124–W127.CrossRefGoogle ScholarPubMed
Allemand, J.-F., Bensimon, D., Lavery, R. & Croquette, V. (1998). Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proceedings of the National Academy of Sciences of the United States of America 95, 14152–14157.CrossRefGoogle ScholarPubMed
Anderson, P. & Bauer, W. (1978). Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry 17, 594–601.CrossRefGoogle ScholarPubMed
Ansari, A. Z., Chael, M. L. & O'Halloran, T. V. (1992). Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-Mer. Nature 355, 87–89.CrossRefGoogle Scholar
Arnott, S. & Selsing, E. (1974). Structures for the polynucleotide complexes poly(dA) with poly(dT) and poly(dT) with poly(dA) with poly (dT). Journal of Molecular Biology 88, 509–521.CrossRefGoogle ScholarPubMed
Bae, S. H., Yun, S. H., Sun, D., Lim, H. M. & Choi, B. S. (2006). Structural and dynamic basis of a supercoiling-responsive DNA element. Nucleic Acids Research 34, 254–261.CrossRefGoogle ScholarPubMed
Bagga, R., Ramesh, N. & Brahmachari, S. K. (1990). Supercoil-induced unusual DNA structures as transcriptional block. Nucleic Acids Research 18, 3363–3369.CrossRefGoogle ScholarPubMed
Balasubramanian, S., Xu, F. & Olson, W. K. (2009). DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophysical Journal 96, 2245–2260.CrossRefGoogle ScholarPubMed
Balasubramanian, S., Hurley, L. H. & Neidle, S. (2011). Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nature Reviews Drug Discovery 10, 261–275.CrossRefGoogle ScholarPubMed
Baldwin, G. S., Brooks, N. J., Robson, R. E., Wynveen, A., Goldar, A., Leikin, S., Seddon, J. M. & Kornyshev, A. A. (2008). DNA double helices recognize mutual sequence homology in a protein free environment. Journal of Physical Chemistry B 112, 1060–1064.CrossRefGoogle Scholar
Bao, X. R., Lee, H. J. & Quake, S. R. (2003). Behavior of complex knots in single DNA molecules. Physical Review Letters 91, 34.CrossRefGoogle ScholarPubMed
Bassett, A., Cooper, S., Wu, C. & Travers, A. (2009). The folding and unfolding of eukaryotic chromatin. Current Opinion in Genetics and Development 19, 159–165.CrossRefGoogle ScholarPubMed
Bates, A. D. & Maxwell, A. (2005). DNA Topology, 2nd edn. New York: Oxford University Press.CrossRefGoogle Scholar
Bates, A. D. & Maxwell, A. (2007). Energy coupling in type II topoisomerases: why do they hydrolyze ATP? Biochemistry 46, 7929–7941.CrossRefGoogle ScholarPubMed
Bates, A. D., Berger, J. M. & Maxwell, A. (2011). The ancestral role of ATP hydrolysis in type II topoisomerases: prevention of DNA double-strand breaks. Nucleic Acids Research 39, 6327–6339.CrossRefGoogle ScholarPubMed
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, 825–847.CrossRefGoogle ScholarPubMed
Belotserkovskii, B. P., De Silva, E., Tornaletti, S., Wang, G., Vasquez, K. M. & Hanawalt, P. C. (2007). A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription. Journal of Biological Chemistry 282, 32433–32441.CrossRefGoogle ScholarPubMed
Benham, C. J. & Mielke, S. P. (2005). DNA mechanics. Annual Review of Biomedical Engineering 7, 21–53.CrossRefGoogle ScholarPubMed
Berg, O. G., Winter, R. B. & Von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20, 6929–6948.CrossRefGoogle ScholarPubMed
Bloomfield, V. A. (1996). DNA condensation. Current Opinion in Structural Biology 6, 334–341.CrossRefGoogle ScholarPubMed
Bloomfield, V. A. (1997). DNA condensation by multivalent cations. Biopolymers 44, 269–282.3.0.CO;2-T>CrossRefGoogle ScholarPubMed
Blot, N., Mavathur, R., Geertz, M., Travers, A. & Muskhelishvili, G. (2006). Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Reports 7, 710–715.CrossRefGoogle ScholarPubMed
Boles, T. C., White, J. H. & Cozzarelli, N. R. (1990). Structure of plectonemically supercoiled DNA. Journal of Molecular Biology 213, 931–951.CrossRefGoogle ScholarPubMed
Bolon, M. K. (2009). The newer flouroquinolones. Infectious Disease Clinics of North America 23, 1027–1051.CrossRefGoogle Scholar
Bond, L. M., Peters, J. P., Becker, N. A., Kahn, J. D. & Maher, L. J. III (2010). Gene repression by minimal lac loops in vivo. Nucleic Acids Research 38, 8072–8082.CrossRefGoogle ScholarPubMed
Boyd, L. B., Atmar, R. L., Randall, G. L., Hamill, R. J., Steffen, D. & Zechiedrich, L. (2008). Increased fluoroquinolone resistance with time in Escherichia coli from >17,000 patients at a large county hospital as a function of culture site, age, sex, and location. BMC Infectious Diseases 8, 35.CrossRefGoogle Scholar
Brooks, C. L., Karplus, M. & Pettitt, B. M. (1988). Advances in Chemical Physics, Proteins: A Theoretical Perspective on Dynamics, Structure, and Thermodynamics, Vol. 71. New York: Wiley.CrossRefGoogle Scholar
Buck, G. R. & Zechiedrich, E. L. (2004). DNA disentangling by type-2 topoisomerases. Journal of Molecular Biology 340, 933–939.CrossRefGoogle ScholarPubMed
Burnier, Y., Weber, C., Flammini, A. & Stasiak, A. (2007). Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases. Nucleic Acids Research 35, 5223–5331.CrossRefGoogle ScholarPubMed
Bustamante, C., Bryant, Z. & Smith, S. B. (2003). Ten years of tension: single-molecule DNA mechanics. Nature 421, 423–427.CrossRefGoogle ScholarPubMed
Călugăreanu, G. (1961). Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants. Czechoslovak Mathematical Journal. 11, 588–625.CrossRefGoogle Scholar
Chaires, J. B. (2006). A thermodynamic signature for drug-DNA binding mode. Archives of Biochemistry and Biophysics 453, 26–31.CrossRefGoogle ScholarPubMed
Champ, P. C., Maurice, S., Vargason, J. M., Camp, T. & Ho, P. S. (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research 32, 6501–6510.CrossRefGoogle Scholar
Chapman, D. L. (1913). A contribution to the theory of electrocapilarity. Philosiphical Magazine Series 25, 475–481.CrossRefGoogle Scholar
Charbonnier, F. & Forterre, P. (1994). Comparison of plasmid topology among mesophilic and thermophilic eubacteria and archaebacteria. Journal of Bacteriology 176, 1251–1259.CrossRefGoogle ScholarPubMed
Chenoweth, D. M. & Dervan, P. B. (2009). Allosteric modulation of DNA by small molecules. Proceedings of the National Academy of Sciences of the United States of America 106, 13175–13179.CrossRefGoogle ScholarPubMed
Cherny, D. I. & Jovin, T. M. (2001). Electron and scanning force microscopy studies of alterations in supercoiled DNA tertiary structure. Journal of Molecular Biology 313, 295–307.CrossRefGoogle ScholarPubMed
Cloutier, T. E. & Widom, J. (2004). Spontaneous sharp bending of double-stranded DNA. Molecular Cell 14, 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 of the United States of America 102, 3645–3650.CrossRefGoogle ScholarPubMed
Corbett, K. D., Schoeffler, A. J., Thomsen, N. D. & Berger, J. M. (2005). The structural basis for substrate specificity in DNA topoisomerase IV. Journal of Molecular Biology 351, 545–561.CrossRefGoogle ScholarPubMed
Corbett, K. D., Benedetti, P. & Berger, J. M. (2007). Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Nature Structural and Molecular Biology 14, 611–619.CrossRefGoogle ScholarPubMed
Cozzarelli, N. R., Boles, T. C. & White, J. H. (1990). Primer on the topology and geometry of DNA supercoiling. In DNA Topology and Its Biological Effects (eds. Cozzarelli, N. R. & Wang, J. C.), pp. 139–184, Woodbury, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Cozzarelli, N. R., Cost, G. J., Nöllmann, M., Viard, T. & Stray, J. E. (2006). Giant proteins that move DNA: bullies of the genomic playground. Nature Reviews Molecular Cell Biology 7, 580–588.CrossRefGoogle ScholarPubMed
Crick, F. H. & Klug, A. (1975). Kinky helix. Nature 255, 530–533.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.CrossRefGoogle ScholarPubMed
Crozat, E., Philippe, N., Lenski, R. E., Geiselmann, J. & Schneider, D. (2005). Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics 169, 523–532.CrossRefGoogle ScholarPubMed
Crozat, E., Winkworth, C., Gaffé, J., Hallin, P. F., Riley, M. A., Lenski, R. E. & Schneider, D. (2010). Parallel genetic and phenotypic evolution of DNA superhelicity in experimental populations of Escherichia coli. Molecular Biology and Evolution 27, 2113–2128.CrossRefGoogle ScholarPubMed
Curuksu, J., Zacharias, M., Lavery, R. & Zakrzewska, K. (2009). Local and global effects of strong bending induced during molecular dynamics simulations. Nucleic Acids Research 37, 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, 685–695.CrossRefGoogle ScholarPubMed
Dai, X., Kloster, M. & Rothman-Denes, L. B. (1998). Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters. Journal of Molecular Biology 283, 43–58.CrossRefGoogle ScholarPubMed
Darcy, I. K., Scharein, R. G. & Stasiak, A. (2008). 3D visualization software to analyze topological outcomes of topoisomerase reactions. Nucleic Acids Research 36, 3515–3521.CrossRefGoogle ScholarPubMed
Deibler, R. W., Rahmati, S., & Zechiedrich, E. L. (2001). Topoisomerase IV, alone, unknots DNA in E. coli. Genes and Development 15, 748–761.CrossRefGoogle ScholarPubMed
Deibler, R. W., Mann, J. K., Sumners, D. W. L. & Zechiedrich, L. (2007). Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Molecular Biology 8, 44.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, 2882–2893.CrossRefGoogle ScholarPubMed
Desai, N. A. & Shankar, V. (2003). Single-strand specific nucleases. FEMS Microbiology Reviews 26, 457–491.CrossRefGoogle ScholarPubMed
Dillon, S. C. & Dorman, C. J. (2010). Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nature Reviews Microbiology 8, 185–195.CrossRefGoogle ScholarPubMed
Dong, K. C. & Berger, J. M. (2007). Structural basis for gate-DNA recognition and bending by type IIa topoisomerases. Nature 450, 1201–1205.CrossRefGoogle ScholarPubMed
Dorman, C. J. (2008). Regulation of transcription in bacteria by DNA supercoiling. In Bacterial Physiology: A Molecular Approach (ed. El-Sharoud, W.), pp. 155–178. Berlin: Springer.CrossRefGoogle Scholar
Dorman, C. J. & Corcoran, C. P. (2009). Bacterial DNA topology and infectious disease. Nucleic Acids Research. 37, 672–678.CrossRefGoogle ScholarPubMed
Dorman, C. J. & Deighan, P. (2003). Regulation of gene expression by histone-like proteins in bacteria. Current Opinion in Genetics and Development 13, 179–184.CrossRefGoogle ScholarPubMed
Drlica, K. & Malik, M. (2003). Fluoroquinolones: action and resistance. Current Topics in Medicinal Chemistry 3, 249–282.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 of the United States of America 102, 5397–5402.CrossRefGoogle ScholarPubMed
Du, Q., Kotlyar, A. & Vologodskii, A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Research 36, 1120–1128.CrossRefGoogle ScholarPubMed
Dumont, S., Cheng, W., Serebrov, V., Beran, R. K., Tinoco, I., Pyle, A. M. & Bustamante, C. (2006). RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature 439, 105–108.CrossRefGoogle ScholarPubMed
Falaschi, A. (2008). Similia similibus: pairing of homologous chromosomes driven by the physicochemical properties of DNA. Human Frontiers Science Program Journal 2, 257–261.Google ScholarPubMed
Feig, M. & Pettitt, B. M. (1988). A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers 48, 199–209.3.0.CO;2-5>CrossRefGoogle Scholar
Ferrándiz, M. J., Martín-Galiano, A. J., Schvartzman, J. B. & De La Campa, A. G. (2010). The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters. Nucleic Acids Research 38, 3570–3581.CrossRefGoogle ScholarPubMed
Fogg, J. M., Kolmakova, N., Rees, I., Magonov, S., Hansma, H., Perona, J. J. & Zechiedrich, E. L. (2006). Exploring writhe in supercoiled minicircle DNA. Journal of Physics: Condensed Matter 18, S145–S159.Google ScholarPubMed
Fogg, J. M., Catanese, D. J. Jr, Randall, G. L., Swick, M. C. & Zechiedrich, L. (2009). Differences between positively and negatively supercoiled DNA that topoisomerases may distinguish. In The Institute for Mathematics and its Applications Volumes in Mathematics and its Applications. Mathematics of DNA Structure, Function and Interactions, Vol. 150 (eds. Benham, C. J., Harvey, S., Olson, W. K., Sumners, D. W. L. & Swigon, D.), pp. 73–122. New York: Springer.Google Scholar
Forterre, P., Gribaldo, S., Gadelle, D. & Serre, M. C. (2007). Origin and evolution of DNA topoisomerases. Biochimie 89, 427–446.CrossRefGoogle ScholarPubMed
Forterre, P. & Gadelle, D. (2009). Phylogenetics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Research 37, 679–692.CrossRefGoogle ScholarPubMed
Forth, S., Deufel, C., Sheinin, M. Y., Daniels, B., Sethna, J. P. & Wang, M. D. (2008). Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules. Physical Review Letters 100, 148301.CrossRefGoogle ScholarPubMed
Fuchs, R. P. P. (1975). In vitro recognition of carcinogen-induced local denaturation sites native DNA by S1 endonuclease from Aspergillus oryzae. Nature 257, 151–152.CrossRefGoogle ScholarPubMed
Fuller, F. (1978). Decomposition of the linking number of a closed ribbon: a problem from molecular biology. Proceedings of the National Academy of Sciences of the United States of America 75, 3557–3561.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
Giudice, E., Varnai, P. & Lavery, R. (2003). Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Research 31, 1434–1443.CrossRefGoogle ScholarPubMed
Gouy, G. J. (1910). Sur la constitution de la charge electrique a la surface d'un electrolyte. Journal de Physique 9, 457–468.Google Scholar
Gowers, D. M. & Halford, S. E. (2003). Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling. EMBO Journal 22, 1410–1418.CrossRefGoogle ScholarPubMed
Gromiha, M. M., Siebers, J. G., Selvaraj, S., Kono, H. & Sarai, A. (2004). Intermolecular and intramolecular readout mechanisms in protein–DNA recognition. Journal of Molecular Biology 337, 285–294.CrossRefGoogle Scholar
Guo, F., Gopaul, D. N. & Van Duyne, G. D. (1997). Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389, 40–46.CrossRefGoogle Scholar
Ha, S. C., Lowenhaupt, K., Rich, A., Kim, Y. G. & Kim, K. K. (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437, 1183–1186.CrossRefGoogle ScholarPubMed
Halford, S. E. & Marko, J. F. (2004). How do site-specific DNA-binding proteins find their targets? Nucleic Acids Research 32, 3040–3052.CrossRefGoogle ScholarPubMed
Halford, S. E., Welsh, A. J. & Szczelkun, M. D. (2004). Enzyme-mediated DNA looping. Annual Review of Biophysics and Biomolecular Structure 33, 1–24.CrossRefGoogle ScholarPubMed
Hanvey, J. C., Shimizu, M. & Wells, R. D. (1988). Intramolecular DNA triplexes in supercoiled plasmids. Proceedings of the National Academy of Science of the United States of America 85, 6292–6296.CrossRefGoogle ScholarPubMed
Hardin, A. H., Sarkar, S. K., Seol, Y., Liou, G. F., Osheroff, N. & Neuman, K. C. (2011). Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification. Nucleic Acids Research (epub ahead of print).CrossRefGoogle 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, 21–29.CrossRefGoogle ScholarPubMed
Heeb, S., Fletcher, M. P., Chhabra, S. R., Diggle, S. P., Williams, P. & Cámara, M. (2011). Quinolones: from antibiotics to autoinducers. FEMS Microbiology Reviews 35, 247–274.CrossRefGoogle ScholarPubMed
Herbert, A., Lowenhaupt, K., Spitzner, J. & Rich, A. (1995). Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proceedings of the National Academy of Sciences of the United States of America 92, 7550–7554.CrossRefGoogle ScholarPubMed
Hudson, B. & Vinograd, J. (1967). Catenated circular molecules in HeLa cell mitochondria. Nature 216, 647–652.CrossRefGoogle ScholarPubMed
Jacob, F. & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3, 318–356.CrossRefGoogle ScholarPubMed
Jaenisch, R. & Levine, A. J. (1973). DNA replication of SV40-infected cells VII. Formation of SV40 catenated and circular dimers. Journal of Molecular Biology 73, 199–212.CrossRefGoogle ScholarPubMed
Jen-Jacobson, L., Engler, L. E. & Jacobson, L. A. (2000). Structural and thermodynamic strategies for site-specific DNA binding proteins. Structure 8, 1015–1023.CrossRefGoogle ScholarPubMed
Jian, H., Schlick, T. & Vologodskii, A. (1998). Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition. Journal of Molecular Biology 284, 287–296.CrossRefGoogle ScholarPubMed
Johnson, D. S., Bai, L., Smith, B. Y., Patel, S. S. & Wang, M. D. (2007). Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell 129, 1299–1309.CrossRefGoogle ScholarPubMed
Kannan, S., Kohlhoff, K. & Zacharias, M. (2006). B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations. Biophysical Journal 91, 2956–2965.CrossRefGoogle ScholarPubMed
Khodursky, A. B., Peter, B. J., Schmid, M. B., Derisi, J., Botstein, D., Brown, P. O. & Cozzarelli, N. R. (2000). Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proceedings of the National Academy of Sciences of the United States of America 97, 9419–9424.CrossRefGoogle ScholarPubMed
Kim, J. L., Nikolov, D. B. & Burley, S. K. (1993a). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520–527.CrossRefGoogle ScholarPubMed
Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. (1993b). Crystal structure of a yeast TBP/TATA -box complex. Nature 365, 512–520.CrossRefGoogle ScholarPubMed
Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. (1994). HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357–369.CrossRefGoogle ScholarPubMed
Kono, H. & Sarai, A. (1999). Structure-based prediction of DNA target sites by regulatory proteins. Proteins 35, 114–131.3.0.CO;2-T>CrossRefGoogle ScholarPubMed
Kornyshev, A. A. & Wynveen, A. (2009). The homology recognition well as an inate property of DNA structure. Proceedings of the National Academy of Sciences of the United States of America 24, 4683–4688.CrossRefGoogle Scholar
Koudelka, G. B. (1998). Recognition of DNA structure by 434 repressor. Nucleic Acids Research 26, 669–675.CrossRefGoogle ScholarPubMed
Koudelka, G. B. & Carlson, P. (1992). DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor. Nature 355, 89–91.CrossRefGoogle ScholarPubMed
Koudelka, G. B., Harrison, S. C. & Ptashne, M. (1987). Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and cro. Nature 326, 886–888.CrossRefGoogle ScholarPubMed
Kouzine, F. & Levens, D. (2007). Supercoil-driven DNA structures regulate genetic transactions. Frontiers in Bioscience 12, 4409–4423.CrossRefGoogle ScholarPubMed
Kouzine, F., Liu, J., Sanford, S., Chung, H.-J. & Levens, D. (2004). The dynamic response of upstream DNA to transcription-generated torsional stress. Nature Structural and Molecular Biology 11, 1092–1100.CrossRefGoogle ScholarPubMed
Kouzine, F., Sanford, S., Elisha-Feil, Z. & Levens, D. (2008). The functional response of upstream DNA to dynamic supercoiling in vivo. Nature Structural and Molecular Biology 15, 146–154.CrossRefGoogle ScholarPubMed
Kramer, P. R. & Sinden, R. R. (1997). Measurement of unrestrained negative supercoiling and topological domain size in living human cells. Biochemistry 36, 3151–3158.CrossRefGoogle ScholarPubMed
Kreuzer, K. N. & Cozzarelli, N. R. (1979). Escherichia coli mutants thermosensitive for deoxyribonucleic acid gyrase subunit A: effects on deoxyribonucleic acid replication, transcription and bacteriophage growth. Journal of Bacteriology 140, 424–435.CrossRefGoogle ScholarPubMed
Kuhn, W. (1934). Über die gestalt fadenförmiger moleküle in Lösungen, Kolloid-Z. 68, 2.CrossRefGoogle Scholar
Kupersztoch, Y. M. & Helinski, D. R. (1973). A catenated DNA molecule as an intermediate in the replication of the resistance transfer factor RK6 in Escherichia coli. Biochemical and Biophysical Research Communications 54, 1451–1459.CrossRefGoogle Scholar
Lankas, F., Lavery, R. & Maddocks, J. H. (2006). Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure 14, 1527–1534.CrossRefGoogle ScholarPubMed
Lankas, F., Sponer, J., Langowski, J. & Cheatham, T. E. (2003). DNA basepair step deformability inferred from molecular dynamics simulations. Biophysical Journal 85, 2872–2883.CrossRefGoogle ScholarPubMed
Lau, P. P. & Gray, H. B. Jr (1979). Extracellular nucleases of Alteromonas espejiana BAL 31.IV. The single strand-specific deoxyriboendonuclease activity as a probe for regions of altered secondary structure in negatively and positively supercoiled closed circular DNA. Nucleic Acids Research 6, 331–357.CrossRefGoogle ScholarPubMed
Léger, J. F., Romano, G., Sarkar, A., Robert, J., Bourdieu, L., Chatenay, D. & Marko, J. F. (1999). Structural transitions of a twisted and stretched DNA molecule. Physical Review Letters 83, 1066–1069.CrossRefGoogle Scholar
Legerski, R. J., Gray, H. B. Jr & Robberson, D. L. (1977). A sensitive endonuclease probe for lesions in deoxyribonucleic acid helix structure produced by carcinogenic or mutagenic agents. Journal of Biological Chemistry 252, 8740–8746.CrossRefGoogle ScholarPubMed
Li, X. Y., Macarthur, S., Bourgon, R., Nix, D., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Hendriks, C. L., Chu, H. C., Ogawa, N., Inwood, W., Sementchenko, V., Beaton, A., Weiszmann, R., Celniker, S. E., Knowles, D. W., Gingeras, T., Speed, T. P., Eisen, M. B. & Biggin, M. D. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biology 6, e27.CrossRefGoogle ScholarPubMed
Lilley, D. M. J. & Higgins, C. F. (1991). Local DNA topology and gene expression: the case of the leu-500 promoter. Molecular Microbiology 5, 779–783.CrossRefGoogle ScholarPubMed
Lim, H. M., Lewis, D. E., Lee, H. J., Liu, M. & Adhya, S. (2003). Effect of varying the supercoiling of DNA on transcription and its regulation. Biochemistry 42, 10718–10725.CrossRefGoogle ScholarPubMed
Lionberger, T. A., Demurtas, D., Witz, G., Dorier, J., Lillian, T., Meyhöfer, E. & Stasiak, A. (2011). Cooperative kinking at distant sites in mechanically stressed DNA. Nucleic Acids Research published online ahead of print.CrossRefGoogle ScholarPubMed
Liu, L. F. & Wang, J. C. (1975). On the degree of unwinding of the DNA helix by ethidium. II. Studies by electron microscopy. Biochimica et Biophysica Acta 395, 401–412.Google ScholarPubMed
Liu, L. F. & Wang, J. C. (1987). Supercoiling of the DNA template during transcription. Proceedings of the National Academy of Sciences of the United States of America 84, 7024–7027.CrossRefGoogle ScholarPubMed
Liu, Z., Mann, J. K., Zechiedrich, E. L. & Chan, H. S. (2006a). Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases. Journal of Molecular Biology 361, 268–285.CrossRefGoogle ScholarPubMed
Liu, Z., Zechiedrich, E. L. & Chan, H. S. (2006b). Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action. Biophysical Journal 90, 2344–2355.CrossRefGoogle ScholarPubMed
Liu, J., Kouzine, F., Nie, Z., Chung, H. J., Elisha-Feil, Z., Weber, A., Zhao, K. & Levens, D. (2006c). The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression. EMBO Journal 25, 2119–2130.CrossRefGoogle ScholarPubMed
Liu, Z., Deibler, R. W., Chan, H. S. & Zechiedrich, L. (2009). The why and how of DNA unlinking. Nucleic Acids Research 37, 661–671.CrossRefGoogle ScholarPubMed
Liu, Z., Zechiedrich, L. & Chan, H. S. (2010a). Local site preference rationalizes disentangling by DNA topoisomerases. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 81, 031902.CrossRefGoogle ScholarPubMed
Liu, Z., Zechiedrich, L. & Chan, H. S. (2010b). Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases. Journal of Molecular Biology 400, 963–982.CrossRefGoogle ScholarPubMed
Liverpool, T. B., Harris, S. A. & Laughton, C. A. (2008). Supercoiling and denaturation of DNA loops. Physical Review Letters 100, 238103.CrossRefGoogle ScholarPubMed
Lockshon, D. & Morris, D. R. (1983). Positively supercoiled plasmid DNA is produced by treatment of Echerichia coli with DNA gyrase inhibitors. Nucleic Acids Research 11, 2999–3017.CrossRefGoogle Scholar
López-García, P. & Forterre, P. (2000). DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles. Bioessays 22, 738–746.3.0.CO;2-5>CrossRefGoogle ScholarPubMed
Love, J. J., Li, X., Chung, J., Dyson, H. J. & Wright, P. E. (2004). The LEF-1 high-mobility group undergoes a disorder-to-order transition upon formation of a complex with cognate DNA. Biochemistry 43, 8725–8734.CrossRefGoogle ScholarPubMed
Lu, F. & Churchward, G. (1994). Conjugative transposition: Tn916 integrase contains two independent DNA binding domains that recognize different DNA sequences. EMBO Journal 13, 1541–1548.CrossRefGoogle ScholarPubMed
Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. (1997). Crystal structure of the nucleosome core partice at 2.8 Å resolution. Nature 389, 251–260.CrossRefGoogle Scholar
Madden, K. R., Stewart, L. & Champoux, J. J. (1995). Preferential binding of human topoisomerase I to superhelical DNA. EMBO Journal 14, 5399–5409.CrossRefGoogle ScholarPubMed
Maerkl, S. J. & Quake, S. R. (2007). A systems approach to measuring the binding energy landscapes of transcription factors. Science 315, 233–237.CrossRefGoogle ScholarPubMed
Maher, L. J. (1998). Mechanisms of DNA bending. Current Opinion in Chemical Biology 2, 688–694.CrossRefGoogle ScholarPubMed
Makarov, V., Feig, M. & Pettitt, B. M. (2002). Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Accounts of Chemical Research 35, 376–384.CrossRefGoogle ScholarPubMed
Manning, G. S. (1969a). Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties. Journal of Chemical Physics 51, 924–933.CrossRefGoogle Scholar
Manning, G. S. (1969b). Limiting laws and counterion condensation in polyelectrolyte solutions. II. Self-diffusion of the small ions. Journal of Chemical Physics 51, 934–938.CrossRefGoogle Scholar
Marko, J. F. (2007). Torque and dynamics of linking number relaxation in stretched supercoiled DNA. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 76, 021926.CrossRefGoogle ScholarPubMed
Marko, J. F. (2009). Micromechanics of single supercoiled DNA molecules. In The Institute for Mathematics and its Applications Volumes in Mathematics and its Applications. Mathematics of DNA Structure, Function and Interactions, vol. 150 (eds. Benham, C. J., Harvey, S., Olson, W. K., Sumners, D. W. L. & Swigon, D.), pp. 225–250. New York: Springer.Google Scholar
Marko, J. F., Feig, M. & Pettitt, B. M. (2003). Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force-field choice. In Metal–Ligand Interactions: Molecular-, Nano-, Micro-, and Macro-systems in Complex Environments (eds. Russo, N., Salahub, D. R. & Witko, M.), pp. 193–204. Dordrecht: Kluwer Academic Press.CrossRefGoogle Scholar
Martincic, D. & Hande, K. R. (2005). Topoisomerase II inhibitors. Cancer Chemotherapy and Biological Response Modifiers 22, 101–121.CrossRefGoogle ScholarPubMed
Marvin, D. A., Spencer, M., Wilkins, M. H. & Hamilton, L. D. (1958). A new configuration of deoxyribonucleic acid. Nature 182, 387–388.CrossRefGoogle ScholarPubMed
Maxwell, A., Burton, N. P. & O'Hagan, N. (2006). High-throughput assays for DNA gyrase and other topoisomerases. Nucleic Acids Research 34, e104.CrossRefGoogle ScholarPubMed
Mccammon, J. A. & Harvey, S. (1987). Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Mcclellan, J. A. & Lilley, D. M. J. (1991). Structural alteration in alternating adenine-thymine sequences in positively supercoiled DNA. Journal of Molecular Biology 219, 145–149.CrossRefGoogle ScholarPubMed
Merlitz, H., Rippe, K., Klenin, K. V. & Langowski, J. (1998). Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophysical Journal 74, 773–779.CrossRefGoogle ScholarPubMed
Mitchell, J. S., Laughton, C. A. & Harris, S. A. (2011). Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Research, epub ahead of print.CrossRefGoogle ScholarPubMed
Modrich, P. (1982). Studies on sequence recognition by type II restriction and modification enzymes. CRC Critical Reviews in Biochemistry 13, 287–323.CrossRefGoogle ScholarPubMed
Musgrave, D., Zhang, X. & Dinger, M. (2003). Archaeal genome organization and stress responses: implications for the origin and evolution of cellular life. Astrobiology 2, 241–253.CrossRefGoogle Scholar
Muskhelishvili, G., Sobetzko, P., Geertz, M. & Berger, M. (2010). General organisational principles of the transcriptional regulation system: a tree or a circle? Molecular BioSystems 6, 662–676.CrossRefGoogle ScholarPubMed
Nelson, H. C. (1995). Structure and function of DNA-binding proteins. Current Opinion in Genetics and Development 5, 180–189.CrossRefGoogle ScholarPubMed
Neuman, K. C., Charvin, G., Bensimon, D. & Croquette, V. (2009). Mechanisms of chiral discrimination by topoisomerase IV. Proceedings of the National Academy of Sciences of the United States of America 106, 6986–6992.CrossRefGoogle ScholarPubMed
Niehus, E., Cheng, E. & Tan, M. (2008). DNA supercoiling-dependent gene regulation in Chlamydia. Journal of Bacteriology 190, 6419–6427.CrossRefGoogle ScholarPubMed
Novick, R. P., Smith, K., Sheehy, R. J. & Murphy, R. J. (1973). A catenated intermediate in plasmid replication. Biochemical and Biophysical Research Communications 54, 1460–1469.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 of the United States of America 95, 11163–11168.CrossRefGoogle ScholarPubMed
Pack, G. R., Wong, L. & Lamm, G. (1999). Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson–Boltzmann calculations. Biopolymers 49, 575–590.3.0.CO;2-J>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, 389–392.CrossRefGoogle ScholarPubMed
Passner, J. M., Ryoo, H. D., Shen, L., Mann, R. S. & Aggarwal, A. K. (1999). Structure of a DNA-bound ultrabithorax-extradenticle homeodomain complex. Nature 397, 714–719.CrossRefGoogle ScholarPubMed
Patel, A., Yakovleva, L., Shuman, S. & Mondragón, A. (2010). Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site. Structure 18, 725–733.CrossRefGoogle ScholarPubMed
Pauling, L. & Corey, R. B. (1953). A proposed structure for the nucleic acids. Proceedings of the National Academy of Sciences of the United States of America 39, 84–97.CrossRefGoogle ScholarPubMed
Pérez, A., Lankas, F., Luque, F. J. & Orozco, M. (2008). Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Research 36, 2379–2394.CrossRefGoogle ScholarPubMed
Peter, B. J., Ullsperger, C., Hiasa, H., Marians, K. J. & Cozzarelli, N. R. (1998). The structure of supercoiled intermediates in DNA replication. Cell 94, 819–827.CrossRefGoogle ScholarPubMed
Peter, B. J., Arsuaga, J., Breier, A. M., Khodursky, A. B., Brown, P. O. & Cozzarelli, N. R. (2004). Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biology 5, R87.CrossRefGoogle ScholarPubMed
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). UCSF Chimera – a visualization system for exploratory research and analysis. Journal of Computational Chemistry 25, 1605–1612.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, 2692–2704.CrossRefGoogle ScholarPubMed
Portugal, J. & Rodríguez-Campos, A. (1996). T7 RNA polymerase cannot transcribe through a highly knotted DNA template. Nucleic Acids Research 24, 4890–4894.CrossRefGoogle ScholarPubMed
Postow, L., Crisona, N. J., Peter, B. J., Hardy, C. D. & Cozzarelli, N. R. (2001). Topological challenges to DNA replication: conformations at the fork. Proceedings of the National Academy of Sciences of the United States of America 98, 8219–8226.CrossRefGoogle ScholarPubMed
Postow, L., Hardy, C. D., Arsuaga, J. & Cozzarelli, N. R. (2004). Topological domain structure of the Escherichia coli chromosome. Genes and Development 18, 1766–1779.CrossRefGoogle ScholarPubMed
Prabakaran, P., Siebers, J. G., Ahmad, S., Gromiha, M. M., Singarayan, M. G. & Sarai, A. (2006). Classification of protein-DNA complexes based on structural descriptors. Structure 14, 1355–1367.CrossRefGoogle ScholarPubMed
Randall, G. L., Pettitt, B. M., Buck, G. R. & Zechiedrich, E. L. (2006). Electrostatics of DNA–DNA juxtapositions: consequences for type II topoisomerase function. Journal of Physics: Condensed Matter 18, S173–S185.Google 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
Reinisch, K. M., Chen, L., Verdine, G. L. & Lipscomb, W. N. (1995). The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82, 143–153.CrossRefGoogle ScholarPubMed
Revyakin, A., Liu, C., Ebright, R. H. & Strick, T. R. (2006). Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314, 1139–1143.CrossRefGoogle ScholarPubMed
Rich, A. & Zhang, S. (2003). Z-DNA: the long road to biological function. Nature Reviews Genetics 4, 566–572.CrossRefGoogle Scholar
Richmond, T. J. & Davey, C. A. (2003). The structure of DNA in the nucleosome core. Nature 423, 145–150.CrossRefGoogle ScholarPubMed
Roberts, R. J. (1995). On base flipping. Cell 82, 9–12.CrossRefGoogle ScholarPubMed
Robicsek, A., Jacoby, G. A. & Hooper, D. C. (2006). The worldwide emergence of plasmid-mediated quinolone resistance. Lancet Infectious Diseases 6, 629–640.CrossRefGoogle ScholarPubMed
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, 1248–1253.CrossRefGoogle ScholarPubMed
Rohs, R., Jin, X., West, S. M., Joshi, R., Honig, B. & Mann, R. S. (2010). Origins of specificity in protein-DNA recognition. Annual Review of Biochemistry 79, 233–269.CrossRefGoogle ScholarPubMed
Rutkauskas, D., Zhan, H., Matthews, K. S., Pavone, F. S. & Vanzi, F. (2009). Tetramer opening in LacI-mediated DNA looping. Proceedings of the National Academy of Sciences of the United States of America 106, 16627–16632.CrossRefGoogle ScholarPubMed
Rybenkov, V. V., Ullsperger, C., Vologodskii, A. & Cozzarelli, N. R. (1997a). Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277, 690–693.CrossRefGoogle ScholarPubMed
Rybenkov, V. V., Vologodskii, A. V. & Cozzarelli, N. R. (1997b). The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucleic Acids Research 25, 1412–1418.CrossRefGoogle ScholarPubMed
Sakakibara, Y., Suzuki, K. & Tomizawa, J.-I. (1976). Formation of catenated molecules by replication of colicin E1 plasmid DNA in cell extracts. Journal of Molecular Biology 108, 569–582.CrossRefGoogle ScholarPubMed
Santalucia, J., Allawai, H. T. & Seneviratne, P. A. (1996). Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555–3562.CrossRefGoogle ScholarPubMed
Sarkar, A., Léger, J. F., Chatenay, D. & Marko, J. F. (2001). Structural transitions in DNA driven by external force and torque. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 63, 051903.CrossRefGoogle ScholarPubMed
Schlick, T. & Olson, W. K. (1992). Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA. Science 257, 1110–1115.CrossRefGoogle ScholarPubMed
Schneider, R., Travers, A. & Muskhelishvili, G. (2000). The expression of the Escherichia coli fis gene is dependent on the superhelical density of DNA. Molecular Microbiology 38, 167–175.CrossRefGoogle ScholarPubMed
Schoeffler, A. & Berger, J. (2008). DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Quarterly Review of Biophysics 41, 61.CrossRefGoogle ScholarPubMed
Schvartzman, J. B. & Stasiak, A. (2004). A topological view of the replicon. EMBO Reports 5, 256–261.CrossRefGoogle ScholarPubMed
Schwartz, T., Rould, M. A., Lowenhaupt, K., Herbert, A. & Rich, A. (1999). Crystal structure of the Zα domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284, 1841–1845.CrossRefGoogle ScholarPubMed
Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I. K., Wang, J. P. & Widom, J. (2006). A genomic code for nucleosome positioning. Nature 442, 772–778.CrossRefGoogle ScholarPubMed
Shanahan, H. P., Garcia, M. A., Jones, S. & Thornton, J. (2004). Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Research 32, 4732–4741.CrossRefGoogle ScholarPubMed
Shimada, J. & Yamakawa, H. (1985). Statistical mechanics of DNA topoisomers. The helical worm-like chain. Journal of Molecular Biology 184, 319–329.CrossRefGoogle ScholarPubMed
Sinden, R. R. (2005). DNA twists and flips. Nature 437, 1097–1098.CrossRefGoogle ScholarPubMed
Sokolov, I. M., Metzler, R., Pant, K. & Williams, M. C. (2005). Target search of N sliding proteins on a DNA. Biophysical Journal 89, 895–902.CrossRefGoogle Scholar
Starostin, E. L. (2005). On the writhing number of a non-closed curves. In Physical and Numerical Models in Knot Theory Including Applications to the Life Sciences (eds. Calvo, J. A., Millett, K. C., Rawdon, E. J. & Stasiak, A.), pp. 525–545. Singapore: World Scientific Publishing.CrossRefGoogle Scholar
Steffen, N. R., Murphy, S. D., Tolleri, L., Hatfield, G. W. & Lathrop, R. H. (2002). DNA sequence and structure: direct and indirect recognition in protein-DNA binding. Bioinformatics 18 (Suppl. 1), S22–S30.CrossRefGoogle ScholarPubMed
Stella, S., Cascio, D. & Johnson, R. C. (2010). The shape of the DNA minor groove directs binding by the DNA-bending protein FIS. Genes and Development 24, 814–826.CrossRefGoogle ScholarPubMed
Strick, R., Strissel, P. L., Gavrilov, K. & Levi-Setti, R. (2001). Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes. Journal of Cell Biology 155, 899–910.CrossRefGoogle ScholarPubMed
Strick, T. R., Allemand, J.-F., Bensimon, D. & Croquette, V. (1998). Behavior of supercoiled DNA. Biophysical Journal 74, 2016–2028.CrossRefGoogle ScholarPubMed
Strick, T. R., Allemand, J. F., Bensimon, D. & Croquette, V. (2000). Stress-induced structural transitions in DNA and proteins. Annual Review of Biophysics and Biomolecular Structure 29, 523–543.CrossRefGoogle ScholarPubMed
Stuchinskaya, T., Mitchenall, L. A., Schoeffler, A. J., Corbett, K. D., Berger, J. M., Bates, A. D. & Maxwell, A. (2009). How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases. Journal of Molecular Biology 385, 1397–1408.CrossRefGoogle ScholarPubMed
Sumners, D. W., Ernst, C., Spengler, S. J. & Cozzarelli, N. R. (1995). Analysis of the mechanism of DNA recombination using tangles. Quarterly Review of Biophysics 28, 253–313.CrossRefGoogle ScholarPubMed
Svozil, D., Sponer, J. E., Marchan, I., Pérez, A., Cheatham, T. E., Forti, F., Luque, F. J., Orozco, M. & Sponer, J. (2008). Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. The Journal of Physical Chemistry B 112, 8188–8197.CrossRefGoogle 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 of the United States of America 103, 9879–9884.CrossRefGoogle ScholarPubMed
Tarini, M., Cignoni, P. & Montani, C. (2006). Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics 12, 1237–1244.CrossRefGoogle ScholarPubMed
Tolstorukov, M. Y., Colasanti, A. V., McCandlish, D. M., Olson, W. K. & Zhurkin, V. B. (2007). A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucelosme positioning. Journal of Molecular Biology 371, 725–738.CrossRefGoogle ScholarPubMed
Travers, A. & Muskhelishvili, G. (2005). DNA supercoiling – a global transcriptional regulator for enterobacterial growth? Nature Reviews Microbiology 3, 157–169.CrossRefGoogle ScholarPubMed
Travers, A. & Muskhelishvili, G. (2007). A common topology for bacterial and eukaryotic transcription initiation? EMBO Reports 8, 147–151.CrossRefGoogle ScholarPubMed
Van Den Broek, B., Lomholt, M. A., Kalisch, S. M., Metzler, R. & Wuite, G. J. (2008). How DNA coiling enhances target localization by proteins. Proceedings of the National Academy of Sciences of the United States of America 105, 15738–15742.CrossRefGoogle ScholarPubMed
Vijayan, V., Zuzow, R. & O'Shea, E. K. (2009). Oscillations in supercoiling drive circadian gene expression in cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America 106, 22564–22568.CrossRefGoogle ScholarPubMed
Vologodskii, A. (2006). Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophysical Journal 90, 1594–1597.CrossRefGoogle ScholarPubMed
Vologodskii, A. & Cozzarelli, N. R. (1996). Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. Biophysical Journal 70, 2548–2556.CrossRefGoogle ScholarPubMed
Vologodskii, A., Zhang, W., Rybenkov, V. V., Podtelezhnikov, A. A., Subramanian, D., Griffith, J. D. & Cozzarelli, N. R. (2001). Mechanism of topology simplification by type II DNA topoisomerases. Proceedings of the National Academy of Sciences of the United States of America 98, 3045–3049.CrossRefGoogle ScholarPubMed
Vologodskii, A. V., Levene, S. D., Klenin, K. V., Frank-Kamenetskii, M. & Cozzarelli, N. R. (1992). Conformational and thermodynamic properties of supercoiled DNA. Journal of Molecular Biology 227, 1224–1243.CrossRefGoogle ScholarPubMed
Wang, A. H., Quigley, G. J., Kolpak, F. J., Crawford, J. L., Van Boom, J. H., Van Der Marel, G. & Rich, A. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680–686.CrossRefGoogle ScholarPubMed
Wang, G. & Vasquez, K. M. (2006). Non-B DNA structure-induced genetic instability. Mutation Research 598, 103–119.CrossRefGoogle ScholarPubMed
Wang, M. D., Schnitzer, M. J., Yin, H., Landick, R., Gelles, J. & Block, S. M. (1998). Force and velocity measured for single molecules of RNA polymerase. Science 282, 902–907.CrossRefGoogle ScholarPubMed
Wang, X., Zhang, X., Mao, C. & Seeman, N. C. (2010). Double-stranded DNA homology produces a physical signature. Proceedings of the National Academy of Sciences of the United States of America 107, 12547–12552.CrossRefGoogle ScholarPubMed
Warren, A. C. & Cook, P. R. (1978). Supercoiling of DNA and nuclear conformation during the cell-cycle. Journal of Cell Science. 30, 211–226.CrossRefGoogle ScholarPubMed
Wereszczynski, J. & Andricioaei, I. (2006). On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension. Proceedings of the National Academy of Sciences of the United States of America 103, 16200–16205.CrossRefGoogle ScholarPubMed
White, J. H. (1969). Self-linking and the Gauss integral in higher dimensions. American Journal of Mathematics 91, 693–728.CrossRefGoogle Scholar
Wiggins, P. A., Phillips, R. & Nelson, P. C. (2005). Exact theory of kinkable elastic polymers. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 71, 1–19.CrossRefGoogle ScholarPubMed
Winter, R. B., Berg, O. G. & Von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry 20, 6961–6977.CrossRefGoogle ScholarPubMed
Winter, R. B. & Von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor-operator interaction: equilibrium measurements. Biochemistry 20, 6948–6960.CrossRefGoogle ScholarPubMed
Woods, R. J., Barrick, J. E., Cooper, T. F., Shrestha, U., Kauth, M. R. & Lenski, R. E. (2011). Second-order selection for evolvability in a large Escherichia coli population. Science 331, 1433–1436.CrossRefGoogle Scholar
Wright, P. E. & Dyson, H. J. (1999). Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293, 321–331.CrossRefGoogle ScholarPubMed
Wuite, G. J., Smith, S. B., Young, M., Keller, D. & Bustmante, C. (2000). Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404, 103–106.CrossRefGoogle ScholarPubMed
Wynveen, A., Lee, D. J., Kornyshev, A. A. & Leikin, S. (2008). Helical coherence of DNA in crystals and solution. Nucleic Acids Research 36, 5540–5551.CrossRefGoogle ScholarPubMed
Xu, Y. C. & Bremer, H. (1997). Winding of the DNA helix by divalent metal ions. Nucleic Acids Research 25, 4067–4071.CrossRefGoogle ScholarPubMed
Yan, J., Kawamura, R. & Marko, J. F. (2005). Statistics of loop formation along double helix DNAs. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 71, 061905.CrossRefGoogle ScholarPubMed
Yan, J. & Marko, J. F. (2004). Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Physical Review Letters 93, 108108.CrossRefGoogle ScholarPubMed
Yang, W. (2010). Topoisomerases and site-specific recombinases: similarities in structure and mechanism. Criticial Reviews in Biochemistry and Molecular Biology 45, 520–534.CrossRefGoogle ScholarPubMed
Yin, H., Wang, M. D., Svoboda, K., Landick, R., Block, S. M. & Gelles, J. (1995). Transcription against an applied force. Science 270, 1653–1657.CrossRefGoogle ScholarPubMed
Zechiedrich, E. L. & Osheroff, N. (1990). Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. The EMBO Journal 9, 4555–4562.CrossRefGoogle ScholarPubMed
Zechiedrich, E. L., Khodursky, A. B., Bachellier, S., Schneider, R., Chen, D., Lilley, D. M. & Cozzarelli, N. R. (2000). Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. Journal of Biological Chemistry 275, 8103–8113.CrossRefGoogle ScholarPubMed
Zechiedrich, L. & Osheroff, N. (2010). Topoisomerase IB-DNA interactions: X marks the spot. Structure 18, 661–663.CrossRefGoogle ScholarPubMed
Zhang, Y. & Crothers, D. M. (2003). Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophysical Journal 84, 136–153.CrossRefGoogle ScholarPubMed
Zhang, Y., Mcewen, A. E., Crothers, D. M. & Levene, S. D. (2006). Statistical-mechanical theory of DNA looping. Biophysical Journal 90, 1903–1912.CrossRefGoogle ScholarPubMed
Zhao, J., Bacolla, A., Wang, G. & Vasquez, K. M. (2010). Non-B DNA structure-induced genetic instability and evolution. Cellular and Molecular Life Sciences 67, 43–62.CrossRefGoogle ScholarPubMed