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3 - Equilibrium large-scale conformational properties of DNA

Published online by Cambridge University Press:  05 March 2015

Alexander Vologodskii
Alexander Vologodskii
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New York University
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Biophysics of DNA , pp. 72 - 136
Publisher: Cambridge University Press
Print publication year: 2015

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References

Abbondanzieri, E. A., Greenleaf, W. J., Shaevitz, J. W., Landick, R. & Block, S. M. (2005). Direct observation of base-pair stepping by RNA polymerase. Nature 438, 460–5.CrossRefGoogle ScholarPubMed
Allison, S. A., Herr, J. C. & Schurr, J. M. (1981). Structure of viral phi 29 DNA condensed by simple triamines: a light-scattering and electron-microscopy study. Biopolymers 20, 469–88.CrossRefGoogle ScholarPubMed
Andersen, E. S., Dong, M., Nielsen, M. M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M. M., Sander, B., Stark, H., Oliveira, C. L. P., Pedersen, J. S., Birkedal, V., Besenbacher, F., Gothelf, K.V. & Kjems, J. (2009). Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–6.CrossRefGoogle ScholarPubMed
Anderson, C. F. & Record, M. T. J. (1990). Ion distributions around DNA and other cylindrical polyions: theoretical description and physical implications. Annu. Rev. Biophys. Biophys. Chem. 19, 423–65.CrossRefGoogle Scholar
Anderson, P. & Bauer, W. (1978). Supercoiling inclosed circular DNA: dependence uponiontype and concentration. Biochemistry 17, 594–601.CrossRefGoogle Scholar
Arscott, P. G., Li, A. Z. & Bloomfield, V. A. (1990). Condensation of DNA by trivalent cations. 1. Effects of DNA length and topology on the size and shape of condensed particles. Biopolymers 30, 30–619.CrossRefGoogle ScholarPubMed
Balasubramanian, S., Xu, F. & Olson, W. K. (2009). DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophys. J. 96, 96–2245.CrossRefGoogle ScholarPubMed
Barkley, M. D. & Zimm, B. H. (1979). Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70, 2991–3007.CrossRefGoogle Scholar
Baumann, C. G., Bloomfield, V. A., Smith, S. B., Bustamante, C., Wang, M. D. & Block, S. M. (2000). Stretching of single collapsed DNA molecules. Biophys. J. 78, 1965–78.CrossRefGoogle ScholarPubMed
Baumann, C. G., Smith, S. B., Bloomfield, V. A. & Bustamante, C. (1997). Ionic effects on the elasticity of single DNA molecules. Proc. Natl. Acad. Sci. U. S. A. 94, 6185–90.CrossRefGoogle ScholarPubMed
Bednar, J., Furrer, P., Katritch, V., Stasiak, A. Z., Dubochet, J. & Stasiak, A. (1995). Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J. Mol. Biol. 254, 579–94.CrossRefGoogle ScholarPubMed
Benham, C. J. (1978). The statistics of superhelicity. J. Mol. Biol. 123, 361–70.CrossRefGoogle ScholarPubMed
Bensimon, D., Dohmi, D. & Mezard, M. (1998). Stretching a heteropolymer. Europhys. Lett. 42, 97–102.CrossRefGoogle Scholar
Binder, K. & Heermann, D. W. (1997). Monte Carlo Simulations in Statistical Physics. Berlin: Springer.CrossRefGoogle Scholar
Bloomfield, V. A. (1996). DNA condensation. Curr. Opin. Struct. Biol. 6, 334–41.CrossRefGoogle ScholarPubMed
Bosaeus, N., El-Sagheer, A. H., Brown, T., Smith, S. B., Akerman, B., Bustamante, C. & Norden, B. (2012). Tension induces a base-paired overstretched DNA conformation. Proc. Natl. Acad. Sci. U.S.A. 109, 15179–84.CrossRefGoogle ScholarPubMed
Bresler, S. E. & Frenkel, Y. I. (1939). The character of thermal motion of long organic chains with reference to the elastic properties of rubber. Zh. Eksp. Teor. Fiz. 9, 1094–106.Google Scholar
Brian, A. A., Frisch, H. L. & Lerman, L. S. (1981). Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition. Biopolymers 20, 1305–28.CrossRefGoogle Scholar
Bryant, Z., Stone, M. D., Gore, J., Smith, S. B., Cozzarelli, N. R. & Bustamante, C. (2003). Structural transitions and elasticity from torque measurements on DNA. Nature 424, 338–41.CrossRefGoogle ScholarPubMed
Bueche, F. (1962). Physical Properties of Polymers. New York: Interscience.Google Scholar
Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. (1994). Entropic elasticity of lambda-phage DNA. Science 265, 1599–600.CrossRefGoogle ScholarPubMed
Cantor, C. R. & Schimmel, P. R. (1980). Biophysical Chemistry. New York: Freeman.Google Scholar
Chan, S. H., Stoddard, B. L. & Xu, S. Y. (2011). Natural and engineered nicking endonucleases – from cleavage mechanism to engineering of strand-specificity. Nucleic Acids Res. 39, 1–18.CrossRefGoogle ScholarPubMed
Charvin, G., Strick, T. R., Bensimon, D. & Croquette, V. (2005). Topoisomerase IV bends and overtwists DNA upon binding. Biophys. J. 89, 384–92.CrossRefGoogle Scholar
Chattoraj, D. K., Gosule, L. C. & Schellman, A. (1978). DNA condensation with polyamines. II. Electron microscopic studies. J. Mol. Biol. 121, 327–37.CrossRefGoogle ScholarPubMed
Chen, J. H. & Seeman, N. C. (1991). Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–3.CrossRefGoogle ScholarPubMed
Chi, Q., Wang, G. & Jiang, J. (2013). The persistence length and length per base of single-stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory. Physica A 392, 1072–9.CrossRefGoogle Scholar
Cloutier, T. E. & Widom, J. (2004). Spontaneous sharp bending of double-stranded DNA. Mol. Cell 14, 355–62.CrossRefGoogle ScholarPubMed
Cluzel, P., Lebrun, A., Heller, C., Lavery, R., Viovy, J. L., Chatenay, D. & Caron, F. (1996). DNA: an extensible molecule. Science 271, 792–4.CrossRefGoogle Scholar
Cocco, S., Yan, J., Leger, J. F., Chatenay, D. & Marko, J. F. (2004). Overstretching and force-driven strand separation of double-helix DNA. Phys. Rev. E 70, 011910.CrossRefGoogle ScholarPubMed
Crick, F. H. & Klug, A. (1975). Kinky helix. Nature 255, 530–3.CrossRefGoogle ScholarPubMed
Crisona, N. J., Strick, T. R., Bensimon, D., Croquette, V. & Cozzarelli, N. R. (2000). Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev. 14, 2881–92.CrossRefGoogle ScholarPubMed
Crothers, D. M., Haran, T. E. & Nadeau, J. G. (1990). Intrinsically bent DNA. J. Biol. Chem. 265, 7093–6.Google ScholarPubMed
Dahlgren, P. R. & Lyubchenko, Y. L. (2002). Atomic force microscopy study of the effects of Mg2+ and other divalent cations on the end-to-end DNA interactions. Biochemistry 41, 11372–8.CrossRefGoogle Scholar
Dekker, N. H., Rybenkov, V. V., Duguet, M., Crisona, N. J., Cozzarelli, N. R., Bensimon, D. & Croquette, V. (2002). The mechanism of type IA topoisomerases. Proc. Natl. Acad. Sci. U.S.A. 99, 12126–31.CrossRefGoogle ScholarPubMed
Depew, R. E. & Wang, J. C. (1975). Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. U. S. A. 72, 4275–9.CrossRefGoogle ScholarPubMed
Diekmann, S. (1987). DNA curvature. In Nucleic Acids and Molecular Biology, eds. F., Eckstein & D., Lilley, 138–56. Berlin: Springer.Google Scholar
Doty, P. & Bunce, B. H. (1952). The molecular weight and shape of desoxypentose nucleic acid. J. Am. Chem. Soc. 74, 5029–34.CrossRefGoogle Scholar
Du, Q., Kotlyar, A. & Vologodskii, A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Res. 36, 1120–8.CrossRefGoogle ScholarPubMed
Du, Q., Livshits, A., Kwiatek, A., Jayaram, M. & Vologodskii, A. (2007). Protein-induced local DNA bends regulate global topology of recombination products. J. Mol. Biol. 368, 170–82.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. Proc. Natl. Acad. Sci. U. S. A. 102, 5397–402.CrossRefGoogle ScholarPubMed
Duguet, M. (1993). The helical repeat of DNA at high temperature. Nucleic Acids Res. 21, 463–8.CrossRefGoogle ScholarPubMed
Flory, P. J. (1953). Principles of Polymer Chemistry. Ithaca, NY: Cornell University Press.Google Scholar
Forde, N. R., Izhaky, D., Woodcock, G. R., Wuite, G. J. & Bustamante, C. (2002). Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 99, 11682–7.CrossRefGoogle ScholarPubMed
Frank-Kamenetskii, M. D., Anshelevich, V. V. & Lukashin, A. V. (1987). Polyelectrolyte model of DNA. Sov. Phys. Usp. 30, 317–30.CrossRefGoogle Scholar
Frank-Kamenetskii, M. D., Lukashin, A. V., Anshelevich, V. V. & Vologodskii, A. V. (1985). Torsional and bending rigidity of the double helix from data on small DNA rings. J. Biomol. Struct. Dyn. 2, 1005–12.CrossRefGoogle ScholarPubMed
Frank-Kamenetskii, M. D., Lukashin, A. V. & Vologodskii, M. D. (1975). Statistical mechanics and topology of polymer chains. Nature 258, 398–402.CrossRefGoogle ScholarPubMed
Fu, H., Chen, H., Marko, J. F. & Yan, J. (2010). Two distinct overstretched DNA states. Nucleic Acids Res. 38, 5594–600.CrossRefGoogle ScholarPubMed
Fu, H., Chen, H., Zhang, X., Qu, Y., Marko, J. F. & Yan, J. (2011). Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching. Nucleic Acids Res. 39, 3473–81.CrossRefGoogle ScholarPubMed
Fu, T. J. & Seeman, N. C. (1993). DNA double-crossover molecules. Biochemistry 32, 3211–20.CrossRefGoogle ScholarPubMed
Fujimoto, B. S. & Schurr, J. M. (1990). Dependence of the torsional rigidity of DNA on base composition. Nature 344, 175–7.CrossRefGoogle ScholarPubMed
Garcia-Ramírez, M. & Subirana, J. A. (1994). Condensation of DNA by basic proteins does not depend on protein composition. Biopolymers 34, 285–92.CrossRefGoogle Scholar
Gavryushov, S. (2009). Mediating role of multivalent cations in DNA electrostatics: an epsilon modified Poisson–Boltzmann study of B-DNA-B-DNA interactions in mixture of NaCl and MgCl2 solutions. J. Phys. Chem. B 113, 2160–9.CrossRefGoogle ScholarPubMed
Geggier, S., Kotlyar, A. & Vologodskii, A. (2011). Temperature dependence of DNA persistence length. Nucleic Acids Res. 39, 1419–26.CrossRefGoogle ScholarPubMed
Geggier, S. & Vologodskii, A. (2010). Sequence dependence of DNA bending rigidity. Proc. Natl. Acad. Sci. U. S. A. 107, 15421–6.CrossRefGoogle ScholarPubMed
Giambasu, G. M., Luchko, T., Herschlag, D., York, D. M. & Case, D. A. (2014). Ion counting from explicit-solvent simulations and 3D-RISM. Biophys. J. 106, 883–94.CrossRefGoogle ScholarPubMed
Goldstein, R. F. & Benight, A. S. (1992). How many numbers are required to specify sequence-dependent properties of polynucleotides?Biopolymers 32, 1679–93.CrossRefGoogle ScholarPubMed
Gore, J., Bryant, Z., Stone, M. D., Nollmann, M., Cozzarelli, N. R. & Bustamante, C. (2006). Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature 439, 100–4.CrossRefGoogle ScholarPubMed
Gosse, C. & Croquette, V. (2002). Magnetic tweezers: micromanipulation and force measurement at the molecularlevel. Biophys. J. 82, 3314–29.CrossRefGoogle Scholar
Gosule, L. C. & Schellman, J. A. (1976). Compact form of DNA induced by spermidine. Nature 259, 259–333.CrossRefGoogle ScholarPubMed
Goulet, I., Zivanovic, Y. & Prunell, A. (1987). Helical repeat of DNA in solution. The V curve method. Nucleic Acids Res. 15, 2803–21.CrossRefGoogle ScholarPubMed
Gray, D. M. & Tinoco, I. (1970). A new approach to the study of sequence-dependent properties of polynucleotides. Biopolymers 9, 223–44.CrossRefGoogle Scholar
Grosberg, A. Y., Erukhimovitch, I. Y. & Shakhnovitch, E. I. (1982). On the theory of psicondensation. Biopolymers 21, 2413–32.CrossRefGoogle Scholar
Grosberg, A. Y. & Zhestkov, A. V. (1985). On the toroidalcondensed state ofclosed circular DNA. J. Biomol. Struct. Dyn. 3, 515–20.CrossRefGoogle ScholarPubMed
Gueron, M. & Weisbuch, G. (1980). Poly-electrolyte theory. 1. Counterion accumulation, site-binding, and their insensitivity to poly-electrolyte shape in solutions containing finite salt concentrations. Biopolymers 19, 353–82.CrossRefGoogle Scholar
Guth, E. & Mark, H. (1934). Zur innermolekularen, Statistik, insbesondere bei Kettenmolekiilen I. Mon. Chem. verwandte Teile anderer Wiss. 63, 93–121.Google Scholar
Hagerman, P. J. (1981). Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers 20, 1503–35.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1988). Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17, 265–86.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1990). Sequence-directed curvature of DNA. Annu. Rev. Biochem. 59, 755–81.CrossRefGoogle ScholarPubMed
Hagerman, P. J. & Zimm, B. H. (1981). Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains. Biopolymers 20, 1481–502.CrossRefGoogle Scholar
Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y. & Yan, H. (2011). DNA origami with complex curvatures in three-dimensional space. Science 332, 342–6.CrossRefGoogle ScholarPubMed
Horowitz, D. S. & Wang, J. C. (1984). Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173, 75–91.CrossRefGoogle ScholarPubMed
Hsiang, M. W. & Cole, R. D. (1977). Structure of histone H1–DNA complex: effect of histone H1 on DNA condensation. Proc. Natl. Acad. Sci. U. S. A. 74, 4852–6.CrossRefGoogle ScholarPubMed
Hud, N. V. & Downing, K. H. (2001). Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: the fine structure of DNA toroids. Proc. Natl. Acad. Sci. USA 98, 14925–30.CrossRefGoogle ScholarPubMed
Hud, N. V. & Vilfan, I. D. (2005). Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size. Annu. Rev. Biophys. Biomol. Struct. 34, 295–318.CrossRefGoogle ScholarPubMed
Huguet, J. M., Bizarro, C. V., Forns, N., Smith, S. B., Bustamante, C. & Ritort, F. (2010). Single-molecule derivation of salt dependent base-pair free energies in DNA. Proc. Natl. Acad. Sci. U. S.A. 107, 15431–6.CrossRefGoogle ScholarPubMed
Jacobson, H. & Stockmayer, W. H. (1950). Intramolecular reaction in polycondensation. I. Theory of linear systems. J. Chem. Phys. 18, 1600–6.CrossRefGoogle Scholar
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, 1299–309.CrossRefGoogle ScholarPubMed
Katritch, V. & Vologodskii, A. (1997). The effect of intrinsic curvature on conformational properties of circular DNA. Biophys. J. 72, 1070–9.CrossRefGoogle ScholarPubMed
Klenin, K. V., Vologodskii, A. V., Anshelevich, V. V., Dykhne, A. M. & Frank-Kamenetskii, M. D. (1988). Effect of excluded volume on topological properties of circular DNA. J. Biomol. Struct. Dyn. 5, 1173–85.CrossRefGoogle ScholarPubMed
Klenin, K. V., Computer simulation of DNA supercoiling. J. Mol. Biol. 217, 413–19.
Klenin, K. V., Vologodskii, A. V., Anshelevich, V. V., Klisko, V. Y., Dykhne, A. M. & Frank-Kamenetskii, M. D. (1989). Variance of writhe for wormlike DNA rings with excluded volume. J. Biomol. Struct. Dyn. 6, 707–14.CrossRefGoogle ScholarPubMed
Korolev, N., Lyubartsev, A. P. & Nordenskiold, L. (1998). Application of polyelectrolyte theories for analysis of DNA melting in the presence of Na+ and Mg2+ ions. Biophys. J. 75, 3041–56.CrossRefGoogle ScholarPubMed
Korolev, N., Lyubartsev, A. P., Rupprecht, A. & Nordenskiold, L. (1999). Competitive binding of Mg2+, Ca2+, Na+, and K+ ions to DNA in oriented DNA fibers: experimental and Monte Carlo simulation results. Biophys. J. 77, 2736–49.CrossRefGoogle Scholar
Kosikov, K. M., Gorin, A. A., Zhurkin, V. B. & Olson, W. K. (1999). DNA stretching and compression: large-scale simulations of double helical structures. J. Mol. Biol. 289, 1301–26.CrossRefGoogle ScholarPubMed
Kovacic, R. T. & van Holde, K. E. (1977). Sedimentation ofhomogeneous double-stranded DNA molecules. Biochemistry 1977, 1490–8.Google Scholar
Kratky, O. & Porod, G. (1949). Rontgenuntersuchung geloster fadenmolekule. J. Royal Neth. Chem. Sci. 68, 1106–22.Google Scholar
Kuhn, W. (1934). Concerning the shape of thread shapes molecules in solution. Kolloid-Z. 68, 2–15.Google Scholar
Laemmli, U. K. (1975). Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine. Proc. Natl. Acad. Sci. U. S. A. 72, 4288–92.CrossRefGoogle ScholarPubMed
Landau, L. & Lifshitz, E. (1951). Statistical Physics. Oxford: Pergamon.Google Scholar
Landau, L. D. & Lifshitz, E. M. 1986. Fluctuations in the curvature of long molecules. In Theory of Elasticity, 396–400. Oxford, Elsevier.Google Scholar
Lang, D. (1973). Regular superstructures of purified DNA in ethanolic solutions. J. Mol. Biol. 78, 247–54.CrossRefGoogle ScholarPubMed
Le Bret, M. (1980). Monte Carlo computation of supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA. Biopolymers 19, 619–37.CrossRefGoogle ScholarPubMed
Le Bret, M. & Zimm, B. H. (1984). Distribution of counterions around acylindricalpolyelectrolyte and Manning's condensation theory. Biopolymers 1984, 287–312.Google Scholar
Lebrun, A. & Lavery, R. (1996). Modelling extreme stretching of DNA. Nucleic Acids Res. 24, 2260–7.CrossRefGoogle ScholarPubMed
Legerski, R. J. & Robberson, D. L. (1985). Analysis and optimization of recombinant DNA joining reactions. J. Mol. Biol. 181, 297–312.CrossRefGoogle ScholarPubMed
Lerman, L. S. (1971). A transition to a compact form of DNA in polymer solutions. Proc. Natl. Acad. Sci. U. S. A. 68, 1886–90.CrossRefGoogle ScholarPubMed
Levene, S. D. & Crothers, D. M. (1986). Ring closure probabilities for DNA fragments by Monte Carlo simulationJ. Mol. Biol. 189, 61–72.CrossRefGoogle ScholarPubMed
Li, W. F., Nordenskiold, L. & Mu, Y. G. (2011). Sequence-specific Mg2+-DNA interactions: a molecular dynamics simulation study. J. Phys. Chem. B 115, 14713–20.CrossRefGoogle ScholarPubMed
Licinio, P. & Guerra, J. C. (2007). Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets. Biophys. J. 92, 2000–6.CrossRefGoogle ScholarPubMed
Lionnet, T., Spiering, M. M., Benkovic, S. J., Bensimon, D. & Croquette, V. (2007). Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism. Proc. Natl. Acad. Sci. U. S. A. 104, 19790–5.CrossRefGoogle ScholarPubMed
Lipfert, J., Kerssemakers, J. W., Jager, T. & Dekker, N. H. (2010). Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA–DNA filaments. Nat. Methods 7, 977–80.CrossRefGoogle ScholarPubMed
Lohman, T. M. & Bjornson, K. P. (1996). Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65, 169–214.CrossRefGoogle ScholarPubMed
Lu, M., Guo, Q., Marky, L. A., Seeman, N. C. & Kallenbach, N. R. (1992). Thermodynamics of DNA branching. J. Mol. Biol. 223, 781–9.CrossRefGoogle ScholarPubMed
Manning, G. S. (1969). Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties. J. Chem. Phys. 51, 924–33.Google Scholar
Mao, C. D., Sun, W. Q., Shen, Z. Y. & Seeman, N. C. (1999). A nanomechanical device based on the B–Z transition of DNA. Nature 397, 144–6.CrossRefGoogle ScholarPubMed
Marko, J. F. & Siggia, E. D. (1995). Stretching DNA. Macromolecules 28, 8759–70.CrossRefGoogle Scholar
McCammon, J. A. & Harvey, S. C. (1987). Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087–92.CrossRefGoogle Scholar
Millar, D. P., Robbins, R. J. & Zewail, A. H. (1980). Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 77, 5593–7.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). J. Mol. Biol. 285, 245–57.CrossRefGoogle Scholar
Moroz, J. D. & Nelson, P. (1998). Entropic elasticity of twist-storing polymers. Macromolecules 31, 6333–47.CrossRefGoogle Scholar
Murphy, M. C., Rasnik, I., Cheng, W., Lohman, T. M. & Ha, T. (2004). Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys. J. 86, 2530–7.CrossRefGoogle ScholarPubMed
Nelson, P. (1998). Sequence-disorder effects on DNA entropic elasticity. Phys. Rev. Lett. 80, 5810–12.CrossRefGoogle Scholar
Odijk, T. (1977). Polyelectrolytes near the rod limit. J. Polym. Sci. Polym. Phys. Ed. 15, 477–83. (1995). Stiff chains and filaments under tension. Macromolecules 28, 7016–18.CrossRefGoogle Scholar
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. Proc. Natl. Acad. Sci. U.S.A. 95, 11163–8.CrossRefGoogle ScholarPubMed
Omabegho, T., Sha, R. & Seeman, N. C. (2009). A bipedal DNA Brownian motor with coordinated legs. Science 324, 67–71.CrossRefGoogle ScholarPubMed
Onsager, L. (1949). The effects of shape on the interaction of colloidal particles. Ann. N. Y. Acad. Sci. 51, 627–59.CrossRefGoogle Scholar
Owczarzy, R., Moreira, B. G., You, Y., Behlke, M. A. & Walder, J. A. (2008). Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochemistry 47, 47–5336.CrossRefGoogle ScholarPubMed
Owczarzy, R., You, Y., Moreira, B. G., Manthey, J. A., Huang, L., Behlke, M. A. & Walder, J. A. (2004). Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 43, 3537–54.CrossRefGoogle ScholarPubMed
Paik, D. H. & Perkins, T. T. (2011). Overstretching DNA at 65 pN does not require peeling from free ends or nicks. J. Am. Chem. Soc. 133, 3219–21.CrossRefGoogle ScholarPubMed
Pease, P. J., Levy, O., Cost, G. J., Gore, J., Ptacin, J. L., Sherratt, D., Bustamante, C. & Cozzarelli, N. R. (2005). Sequence-directed DNA translocation by purified FtsK. Science 307, 586–90.CrossRefGoogle ScholarPubMed
Peck, L. J. & Wang, J. C. (1981). Sequence dependence of the helical repeat of DNA in solution. Nature 292, 375–8.CrossRefGoogle ScholarPubMed
Peterlin, A. (1953). Light scattering by very stiff chain molecules. Nature 171, 259–60.CrossRefGoogle Scholar
Peters, J. P. & Maher, L. J. I. (2010). DNA curvature and flexibility in vitro and in vivo. Q. Rev. Biophys. 43, 1–41.
Podtelezhnikov, A. A., Mao, C., Seeman, N. C. & Vologodskii, A. V. (2000). Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophys. J. 79, 2692–704.CrossRefGoogle ScholarPubMed
Podtelezhnikov, A. A. & Vologodskii, A. V. (2000). Dynamics of small loops in DNA molecules. Macromolecules 33, 2767–71.CrossRefGoogle Scholar
Post, C. B. & Zimm, B. H. (1979). Internal condensation of a single DNA molecule. Biopolymers 18, 18–1487.CrossRefGoogle Scholar
Protozanova, E., Yakovchuk, P. & Frank-Kamenetskii, M. D. (2004). Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342, 775–85.CrossRefGoogle ScholarPubMed
Rau, D. C., Lee, B. & Parsegian, V. A. (1984). Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices. Proc. Natl. Acad. Sci. U. S. A. 81, 2621–5.CrossRefGoogle ScholarPubMed
Revet, B. & Fourcade, A. (1998). Short unligated sticky ends enable the observation of circularised DNA by atomic force and electron microscopies. Nucleic Acids Res. 26, 2092–7.CrossRefGoogle ScholarPubMed
Rief, M., Clausen-Schaumann, H. & Gaub, H. E. (1999). Sequence-dependent mechanics of single DNA molecules. Nat. Struct. Biol. 6, 346–9.Google ScholarPubMed
Rothemund, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302.CrossRefGoogle ScholarPubMed
Rouzina, I. & Bloomfield, V. A. (1996). Macroion attraction due to electrostatic correlation between screening counterions. 1. Mobile surface-adsorbed ions and diffuse ion cloud. J. Phys. Chem. 100, 9977–89.CrossRefGoogle Scholar
Rouzina, I. (2001). Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys. J. 80, 882–93.Google ScholarPubMed
Rybenkov, V. V., Cozzarelli, N. R. & Vologodskii, A. V. (1993). Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. U. S. A. 90, 5307–11.CrossRefGoogle ScholarPubMed
Rybenkov, V. V, Vologodskii, A. V. & Cozzarelli, N. R. (1997). The effect of ionic conditions on DNA helical repeat, effective diameter, and free energy of supercoiling. Nucleic Acids Res. 25, 1412–18.CrossRefGoogle ScholarPubMed
Saleh, O. A., Perals, C., Barre, F. X. & Allemand, J. F. (2004). Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment. EMBO J. 23, 2430–9.CrossRefGoogle Scholar
SantaLucia, J., Jr. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U. S. A. 95, 1460–5.CrossRefGoogle ScholarPubMed
Schellman, J. A. (1974). Flexibility of DNA. Biopolymers 13, 217–26.CrossRefGoogle ScholarPubMed
Schellman, J. A. & Harvey, S. C. (1995). Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys. Chem. 55, 95–114.CrossRefGoogle ScholarPubMed
Schurr, J. M., Babcock, H. P. & Gebe, J. A. (1995). Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs. Biopolymers 36, 633–41.CrossRefGoogle ScholarPubMed
Seeman, N. C. (1982). Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–47.CrossRefGoogle ScholarPubMed
Seeman, N. C. (2010). Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87.CrossRefGoogle ScholarPubMed
Shaw, S. Y. & Wang, J. C. (1993). Knotting of a DNA chain during ring closure. Science 260, 533–6.CrossRefGoogle ScholarPubMed
Shen, Z., Yan, H., Wang, T. & Seeman, N. C. (2004). Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology. J. Am. Chem. Soc. 126, 1666–74.CrossRefGoogle ScholarPubMed
Sherman, W. B. & Seeman, N. C. (2004). A precisely controlled DNA biped walking device. Nano Lett. 4, 1203–7.CrossRefGoogle Scholar
Shih, W. M., Quispe, J. D. & Joyce, G. F. (2004). A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618–21.CrossRefGoogle ScholarPubMed
Shimada, J. & Yamakawa, H. (1984). Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17, 689–98.CrossRefGoogle Scholar
Shimada, J. (1988). Moments for DNA topoisomers: the helical wormlike chain. Biopolymers 27, 657–73.Google ScholarPubMed
Shin, J. S. & Pierce, N. A. (2004). A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126, 10834–5.CrossRefGoogle ScholarPubMed
Shokri, L., McCauley, M. J., Rouzina, I. & Williams, M. C. (2008). DNA overstretching in the presence of glyoxal: structural evidence of force-induced DNA melting. Biophys. J. 95, 1248–55.CrossRefGoogle ScholarPubMed
Shore, D. & Baldwin, R. L. (1983a). Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170, 957–81.Google ScholarPubMed
Shore, D. (1983b). Energetics of DNA twisting. II. Topoisomer analysis. J. Mol. Biol. 170, 983–1007.CrossRefGoogle ScholarPubMed
Shore, D., Langowski, J. & Baldwin, R. L. (1981). DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. U. S. A. 78, 4833–7.CrossRefGoogle ScholarPubMed
Shure, M. & Vinograd, J. (1976). The number of superhelical turns in native virion SV40 DNA and minicol DNA determined by the band counting method. Cell 8, 215–26.CrossRefGoogle ScholarPubMed
Skolnick, J. & Fixman, M. (1977). Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules 10, 944–8.CrossRefGoogle Scholar
Smith, D. E., Tans, S. J., Smith, S. B., Grimes, S., Anderson, D. L. & Bustamante, C. (2001). The bacteriophage straight phi29 portal motor can package DNA against a large internal force. Nature 413, 748–52.CrossRefGoogle ScholarPubMed
Smith, S. B., Cui, Y. & Bustamante, C. (1996). Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795–9.CrossRefGoogle ScholarPubMed
Smith, S. B., Finzi, L. & Bustamante, C. (1992). Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 1122–6.CrossRefGoogle ScholarPubMed
Spink, C. H., Ding, L., Yang, Q., Sheardy, R. D. & Seeman, N. C. (2009). Thermodynamics of forming a parallel DNA crossover. Biophys. J. 97, 528–38.CrossRefGoogle ScholarPubMed
Stigter, D. (1977). Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers 16, 1435–48.CrossRefGoogle Scholar
Stigter, D. (1978). Comparison of Mannings polyelectrolyte theory with cylindrical Gouy model. J. Phys. Chem. 82, 1603–6.CrossRefGoogle Scholar
Stigter, D. (1995). Evaluation of the counterion condensation theory of polyelectrolytes. Biophys. J. 69, 380–8.CrossRefGoogle ScholarPubMed
Stone, M. D., Bryant, Z., Crisona, N. J., Smith, S. B., Vologodskii, A., Bustamante, C. & Cozzarelli, N. R. (2003). Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc. Natl. Acad. Sci. U. S. A. 100, 8654–9.CrossRefGoogle ScholarPubMed
Strauss, F., Gaillard, C. & Prunell, A. (1981). Helical periodicity of DNA, poly(dA).poly(dT) and poly(dA-dT). poly(dA-dT) in solution. Eur. J. Biochem. 118, 215–22.Google ScholarPubMed
Strick, T. R., Allemand, J. F., Bensimon, D., Bensimon, A. & Croquette, V. (1996). The elasticity of a single supercoiled DNA molecule. Science 271, 1835–7.CrossRefGoogle ScholarPubMed
Strick, T. R., Allemand, J. F., Bensimon, D. & Croquette, V. (1998). Behavior of supercoiled DNA. Biophys. J. 74, 2016–28.CrossRefGoogle ScholarPubMed
Strick, T. R., Croquette, V. & Bensimon, D. (2000). Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature 404, 901–4.CrossRefGoogle ScholarPubMed
Svoboda, K. & Block, S. M. (1994). Biological applications of optical forces. Annu. Rev. Biophys. Biomol. Struct. 23, 247–85.CrossRefGoogle ScholarPubMed
Tagashira, H., Morita, M. & Ohyama, T. (2002). Multimerization of restriction fragments by magnesium-mediated stable base pairing between overhangs: a cause of electrophoretic mobility shift. Biochemistry 41, 12217–23.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. J. Mol. Biol. 212, 363–76.CrossRefGoogle Scholar
Trifonov, E. N., Tan, R. K. Z. & Harvey, S. C. (1988). Static persistence length of DNA. In DNA Bending and Curvature, eds. W. K., Olson, M. H., Sarma, R. H., Sarma & M., Sundaralingam, 243–53. New York: denine.Google Scholar
Upholt, W. B., Gray, H. B., Jr. & Vinograd, J. (1971). Sedimentation velocity behavior of closed circular SV40 DNA as a function of superhelix density, ionic strength, counterion and temperature. J. Mol. Biol. 62, 21–38.CrossRefGoogle ScholarPubMed
van den Broek, B., Noom, M. C., van Mameren, J., Battle, C., Mackintosh, F. C. & Wuite, G. J. (2010). Visualizing the formation and collapse of DNA toroids. Biophys. J. 98, 1902–10.CrossRefGoogle ScholarPubMed
van Loenhout, M. T., de Grunt, M. V. & Dekker, C. (2012). Dynamics of DNA supercoils. Science 338, 338–94.CrossRefGoogle ScholarPubMed
van Mameren, J., Gross, P., Farge, G., Hooijman, P., Modesti, M., Falkenberg, M., Wuite, G. J. & Peterman, E. J. (2009). Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging. Proc. Natl. Acad. Sci. U. S. A. 106, 18231–6.CrossRefGoogle ScholarPubMed
Vologodskaia, M. & Vologodskii, A. (2002). Contribution of the intrinsic curvature to measured DNA persistence length. J. Mol. Biol. 317, 205–13.CrossRefGoogle ScholarPubMed
Vologodskii, A. (2006). Simulation of equilibrium and dynamic properties of large DNA molecules. In Computational Studies of DNA and RNA, eds. F., Lankas & J., Sponer, 579–604. Dordrecht: Springer.Google Scholar
Vologodskii, A. (2012). Bridged DNA circles: a new model system to study DNA topology. Macromolecules 45, 45–4333.CrossRefGoogle Scholar
Vologodskii, A. & Frank-Kamenetskii, M. (2013). Strong bending of the DNA double helix. Nucleic Acids Res. 41, 6785–92.CrossRefGoogle ScholarPubMed
Vologodskii, A. & Rybenkov, V. V. (2009). Simulation of DNA catenanes. Phys. Chem. Chem. Phys. 11, 10543–52.CrossRefGoogle ScholarPubMed
Vologodskii, A. V. (1994). DNA extension under the action of an external force. Macromolecules 27, 27–5623.CrossRefGoogle Scholar
Vologodskii, A. V., Amirikyan, B. R., Lyubchenko, Y. L. & Frank-Kamenetskii, M. D. (1984). Allowance for heterogeneous stacking in the DNA helix–coil transition theory. J. Biomol. Struct. Dyn. 2, 131–48.CrossRefGoogle ScholarPubMed
Vologodskii, A. V., Anshelevich, V. V., Lukashin, A. V. & Frank-Kamenetskii, M. D. (1979). Statistical mechanics of supercoils and the torsional stiffness of the DNA. Nature 280, 294–8.CrossRefGoogle ScholarPubMed
Vologodskii, A. V. & Cozzarelli, N. R. (1995). Modeling of long-range electrostatic interactions in DNA. Biopolymers 35, 289–96.CrossRefGoogle ScholarPubMed
Vologodskii, A. V., Lukashin, A. V. & Frank-Kamenetskii, M. D. (1975). Topological interaction between polymer chains. Sov. Phys. JETP 40, 932–6.Google Scholar
Vologodskii, A. V., Lukashin, A. V., Frank-Kamenetskii, M. D. & Anshelevich, V. V. (1974). Problem of knots in statistical mechanics of polymer chains. Sov. Phys. JETP 39, 1059–63.Google Scholar
Vologodskii, A. V. & Marko, J. F. (1997). Extension of torsionally stressed DNA by external force. Biophys. J. 73, 123–32.CrossRefGoogle ScholarPubMed
Wahl, P., Paoletti, J. & Le Pecq, J. B. (1970). Decay of fluorescence emission anisotropy of the ethidium bromide–DNA complex. Evidence for an internal motion in DNA. Proc. Natl. Acad. Sci. U.S.A. 65, 417–21.CrossRefGoogle Scholar
Wang, J. C. (1969). Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. J. Mol. Biol. 43, 25–39.CrossRefGoogle ScholarPubMed
Wang, J. C. (1979). Helical repeat of DNA in solution. Proc. Natl. Acad. Sci. U. S. A. 76, 200–3.CrossRefGoogle ScholarPubMed
Wang, J. C. & Davidson, N. (1966). Thermodynamic and kinetic studies on the interconversion between the linear and circular forms of phage lambda DNA. J. Mol. Biol. 15, 111–23.CrossRefGoogle ScholarPubMed
Wang, J. C. (1968). Cyclization of phage DNAs. Cold Spring Harbor Symp. Quant. Biol. 33, 409–15.CrossRefGoogle ScholarPubMed
Wang, M. D., Yin, H., Landick, R., Gelles, J. & Block, S. M. (1997). Stretching DNA with optical tweezers. Biophys. J. 72, 1335–46.CrossRefGoogle ScholarPubMed
Wang, X., Zhang, X., Mao, C. & Seeman, N. C. (2010). Double-stranded DNA homology produces a physical signature. Proc. Natl. Acad. Sci. U. S. A. 107, 12547–52.Google ScholarPubMed
Watson, J. D. & Crick, F. H. C. (1953). The structure of DNA. Nature 171, 123–31.Google Scholar
Widom, J. & Baldwin, R. L. (1980). Cation-induced toroidal condensation of DNA – studies with Co3+(NH3)6. J. Mol. Biol. 144, 431–53.CrossRefGoogle ScholarPubMed
Wiggins, P. A., Phillips, R. & Nelson, P. C. (2005). Exact theory of kinkable elastic polymers. Phys. Rev.E 71, 021909.CrossRefGoogle ScholarPubMed
Williams, M. C., Rouzina, I. & Bloomfield, V. A. (2002). Thermodynamics of DNA interactions from single molecule stretching experiments. Acc. Chem. Res. 35, 159–66.CrossRefGoogle ScholarPubMed
Yakovchuk, P., Protozanova, E. & Frank-Kamenetskii, M. D. (2006). Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34, 564–74.CrossRefGoogle ScholarPubMed
Yan, H., LaBean, T. H., Feng, L. & Reif, J. H. (2003). Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices. Proc. Natl. Acad. Sci. U. S. A. 100, 8103–8.CrossRefGoogle ScholarPubMed
Yan, J. & Marko, J. F. (2004). Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93, 108108.CrossRefGoogle ScholarPubMed
Yin, H., Wang, M. D., Svoboda, K., Landick, R., Block, S. M. & Gelles, J. (1995). Transcription against an applied force. Science 270, 1653–7.CrossRefGoogle ScholarPubMed
Yoo, J. & Aksimentiev, A. (2012). Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations. J. Phys. Chem. B 116, 12946–54.CrossRefGoogle ScholarPubMed
Yurke, B., Turberfield, A. J., Mills, A. P., Simmel, F. C. & Neumann, J. L. (2000). A DNA-fuelled molecular machine made of DNA. Nature 406, 605–8.CrossRefGoogle ScholarPubMed
Zhang, X., Chen, H., Fu, H., Doyle, P. S. & Yan, J. (2012). Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements. Proc. Natl. Acad. Sci. U.S.A. 109, 8103–8.Google ScholarPubMed
Zhang, X., Chen, H., Le, S., Rouzina, I., Doyle, P. S. & Yan, J. (2013). Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry. Proc. Natl. Acad. Sci. U. S. A. 110, 3865–70.Google ScholarPubMed
Zhurkin, V. B., Lysov, Y. P. & Ivanov, V. I. (1979). Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res. 6, 1081–96.CrossRefGoogle ScholarPubMed

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