Skip to main content Accessibility help
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 1
  • Print publication year: 2015
  • Online publication date: March 2015

3 - Equilibrium large-scale conformational properties of DNA

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.
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.
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.
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.
Anderson, P. & Bauer, W. (1978). Supercoiling inclosed circular DNA: dependence uponiontype and concentration. Biochemistry 17, 594–601.
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.
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.
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.
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.
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.
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.
Benham, C. J. (1978). The statistics of superhelicity. J. Mol. Biol. 123, 361–70.
Bensimon, D., Dohmi, D. & Mezard, M. (1998). Stretching a heteropolymer. Europhys. Lett. 42, 97–102.
Binder, K. & Heermann, D. W. (1997). Monte Carlo Simulations in Statistical Physics. Berlin: Springer.
Bloomfield, V. A. (1996). DNA condensation. Curr. Opin. Struct. Biol. 6, 334–41.
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.
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.
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.
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.
Bueche, F. (1962). Physical Properties of Polymers. New York: Interscience.
Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. (1994). Entropic elasticity of lambda-phage DNA. Science 265, 1599–600.
Cantor, C. R. & Schimmel, P. R. (1980). Biophysical Chemistry. New York: Freeman.
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.
Charvin, G., Strick, T. R., Bensimon, D. & Croquette, V. (2005). Topoisomerase IV bends and overtwists DNA upon binding. Biophys. J. 89, 384–92.
Chattoraj, D. K., Gosule, L. C. & Schellman, A. (1978). DNA condensation with polyamines. II. Electron microscopic studies. J. Mol. Biol. 121, 327–37.
Chen, J. H. & Seeman, N. C. (1991). Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–3.
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.
Cloutier, T. E. & Widom, J. (2004). Spontaneous sharp bending of double-stranded DNA. Mol. Cell 14, 355–62.
Cluzel, P., Lebrun, A., Heller, C., Lavery, R., Viovy, J. L., Chatenay, D. & Caron, F. (1996). DNA: an extensible molecule. Science 271, 792–4.
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.
Crick, F. H. & Klug, A. (1975). Kinky helix. Nature 255, 530–3.
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.
Crothers, D. M., Haran, T. E. & Nadeau, J. G. (1990). Intrinsically bent DNA. J. Biol. Chem. 265, 7093–6.
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.
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.
Depew, R. E. & Wang, J. C. (1975). Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. U. S. A. 72, 4275–9.
Diekmann, S. (1987). DNA curvature. In Nucleic Acids and Molecular Biology, eds. F., Eckstein & D., Lilley, 138–56. Berlin: Springer.
Doty, P. & Bunce, B. H. (1952). The molecular weight and shape of desoxypentose nucleic acid. J. Am. Chem. Soc. 74, 5029–34.
Du, Q., Kotlyar, A. & Vologodskii, A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Res. 36, 1120–8.
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.
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.
Duguet, M. (1993). The helical repeat of DNA at high temperature. Nucleic Acids Res. 21, 463–8.
Flory, P. J. (1953). Principles of Polymer Chemistry. Ithaca, NY: Cornell University Press.
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.
Frank-Kamenetskii, M. D., Anshelevich, V. V. & Lukashin, A. V. (1987). Polyelectrolyte model of DNA. Sov. Phys. Usp. 30, 317–30.
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.
Frank-Kamenetskii, M. D., Lukashin, A. V. & Vologodskii, M. D. (1975). Statistical mechanics and topology of polymer chains. Nature 258, 398–402.
Fu, H., Chen, H., Marko, J. F. & Yan, J. (2010). Two distinct overstretched DNA states. Nucleic Acids Res. 38, 5594–600.
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.
Fu, T. J. & Seeman, N. C. (1993). DNA double-crossover molecules. Biochemistry 32, 3211–20.
Fujimoto, B. S. & Schurr, J. M. (1990). Dependence of the torsional rigidity of DNA on base composition. Nature 344, 175–7.
Garcia-Ramírez, M. & Subirana, J. A. (1994). Condensation of DNA by basic proteins does not depend on protein composition. Biopolymers 34, 285–92.
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.
Geggier, S., Kotlyar, A. & Vologodskii, A. (2011). Temperature dependence of DNA persistence length. Nucleic Acids Res. 39, 1419–26.
Geggier, S. & Vologodskii, A. (2010). Sequence dependence of DNA bending rigidity. Proc. Natl. Acad. Sci. U. S. A. 107, 15421–6.
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.
Goldstein, R. F. & Benight, A. S. (1992). How many numbers are required to specify sequence-dependent properties of polynucleotides?Biopolymers 32, 1679–93.
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.
Gosse, C. & Croquette, V. (2002). Magnetic tweezers: micromanipulation and force measurement at the molecularlevel. Biophys. J. 82, 3314–29.
Gosule, L. C. & Schellman, J. A. (1976). Compact form of DNA induced by spermidine. Nature 259, 259–333.
Goulet, I., Zivanovic, Y. & Prunell, A. (1987). Helical repeat of DNA in solution. The V curve method. Nucleic Acids Res. 15, 2803–21.
Gray, D. M. & Tinoco, I. (1970). A new approach to the study of sequence-dependent properties of polynucleotides. Biopolymers 9, 223–44.
Grosberg, A. Y., Erukhimovitch, I. Y. & Shakhnovitch, E. I. (1982). On the theory of psicondensation. Biopolymers 21, 2413–32.
Grosberg, A. Y. & Zhestkov, A. V. (1985). On the toroidalcondensed state ofclosed circular DNA. J. Biomol. Struct. Dyn. 3, 515–20.
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.
Guth, E. & Mark, H. (1934). Zur innermolekularen, Statistik, insbesondere bei Kettenmolekiilen I. Mon. Chem. verwandte Teile anderer Wiss. 63, 93–121.
Hagerman, P. J. (1981). Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers 20, 1503–35.
Hagerman, P. J. (1988). Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17, 265–86.
Hagerman, P. J. (1990). Sequence-directed curvature of DNA. Annu. Rev. Biochem. 59, 755–81.
Hagerman, P. J. & Zimm, B. H. (1981). Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains. Biopolymers 20, 1481–502.
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.
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.
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.
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.
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.
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.
Jacobson, H. & Stockmayer, W. H. (1950). Intramolecular reaction in polycondensation. I. Theory of linear systems. J. Chem. Phys. 18, 1600–6.
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.
Katritch, V. & Vologodskii, A. (1997). The effect of intrinsic curvature on conformational properties of circular DNA. Biophys. J. 72, 1070–9.
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.
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.
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.
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.
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.
Kovacic, R. T. & van Holde, K. E. (1977). Sedimentation ofhomogeneous double-stranded DNA molecules. Biochemistry 1977, 1490–8.
Kratky, O. & Porod, G. (1949). Rontgenuntersuchung geloster fadenmolekule. J. Royal Neth. Chem. Sci. 68, 1106–22.
Kuhn, W. (1934). Concerning the shape of thread shapes molecules in solution. Kolloid-Z. 68, 2–15.
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.
Landau, L. & Lifshitz, E. (1951). Statistical Physics. Oxford: Pergamon.
Landau, L. D. & Lifshitz, E. M. 1986. Fluctuations in the curvature of long molecules. In Theory of Elasticity, 396–400. Oxford, Elsevier.
Lang, D. (1973). Regular superstructures of purified DNA in ethanolic solutions. J. Mol. Biol. 78, 247–54.
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.
Le Bret, M. & Zimm, B. H. (1984). Distribution of counterions around acylindricalpolyelectrolyte and Manning's condensation theory. Biopolymers 1984, 287–312.
Lebrun, A. & Lavery, R. (1996). Modelling extreme stretching of DNA. Nucleic Acids Res. 24, 2260–7.
Legerski, R. J. & Robberson, D. L. (1985). Analysis and optimization of recombinant DNA joining reactions. J. Mol. Biol. 181, 297–312.
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.
Levene, S. D. & Crothers, D. M. (1986). Ring closure probabilities for DNA fragments by Monte Carlo simulationJ. Mol. Biol. 189, 61–72.
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.
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.
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.
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.
Lohman, T. M. & Bjornson, K. P. (1996). Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65, 169–214.
Lu, M., Guo, Q., Marky, L. A., Seeman, N. C. & Kallenbach, N. R. (1992). Thermodynamics of DNA branching. J. Mol. Biol. 223, 781–9.
Manning, G. S. (1969). Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties. J. Chem. Phys. 51, 924–33.
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.
Marko, J. F. & Siggia, E. D. (1995). Stretching DNA. Macromolecules 28, 8759–70.
McCammon, J. A. & Harvey, S. C. (1987). Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.
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.
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.
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.
Moroz, J. D. & Nelson, P. (1998). Entropic elasticity of twist-storing polymers. Macromolecules 31, 6333–47.
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.
Nelson, P. (1998). Sequence-disorder effects on DNA entropic elasticity. Phys. Rev. Lett. 80, 5810–12.
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.
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.
Omabegho, T., Sha, R. & Seeman, N. C. (2009). A bipedal DNA Brownian motor with coordinated legs. Science 324, 67–71.
Onsager, L. (1949). The effects of shape on the interaction of colloidal particles. Ann. N. Y. Acad. Sci. 51, 627–59.
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.
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.
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.
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.
Peck, L. J. & Wang, J. C. (1981). Sequence dependence of the helical repeat of DNA in solution. Nature 292, 375–8.
Peterlin, A. (1953). Light scattering by very stiff chain molecules. Nature 171, 259–60.
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.
Podtelezhnikov, A. A. & Vologodskii, A. V. (2000). Dynamics of small loops in DNA molecules. Macromolecules 33, 2767–71.
Post, C. B. & Zimm, B. H. (1979). Internal condensation of a single DNA molecule. Biopolymers 18, 18–1487.
Protozanova, E., Yakovchuk, P. & Frank-Kamenetskii, M. D. (2004). Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342, 775–85.
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.
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.
Rief, M., Clausen-Schaumann, H. & Gaub, H. E. (1999). Sequence-dependent mechanics of single DNA molecules. Nat. Struct. Biol. 6, 346–9.
Rothemund, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302.
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.
Rouzina, I. (2001). Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys. J. 80, 882–93.
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.
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.
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.
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.
Schellman, J. A. (1974). Flexibility of DNA. Biopolymers 13, 217–26.
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.
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.
Seeman, N. C. (1982). Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–47.
Seeman, N. C. (2010). Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87.
Shaw, S. Y. & Wang, J. C. (1993). Knotting of a DNA chain during ring closure. Science 260, 533–6.
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.
Sherman, W. B. & Seeman, N. C. (2004). A precisely controlled DNA biped walking device. Nano Lett. 4, 1203–7.
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.
Shimada, J. & Yamakawa, H. (1984). Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17, 689–98.
Shimada, J. (1988). Moments for DNA topoisomers: the helical wormlike chain. Biopolymers 27, 657–73.
Shin, J. S. & Pierce, N. A. (2004). A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126, 10834–5.
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.
Shore, D. & Baldwin, R. L. (1983a). Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170, 957–81.
Shore, D. (1983b). Energetics of DNA twisting. II. Topoisomer analysis. J. Mol. Biol. 170, 983–1007.
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.
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.
Skolnick, J. & Fixman, M. (1977). Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules 10, 944–8.
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.
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.
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.
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.
Stigter, D. (1977). Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers 16, 1435–48.
Stigter, D. (1978). Comparison of Mannings polyelectrolyte theory with cylindrical Gouy model. J. Phys. Chem. 82, 1603–6.
Stigter, D. (1995). Evaluation of the counterion condensation theory of polyelectrolytes. Biophys. J. 69, 380–8.
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.
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.
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.
Strick, T. R., Allemand, J. F., Bensimon, D. & Croquette, V. (1998). Behavior of supercoiled DNA. Biophys. J. 74, 2016–28.
Strick, T. R., Croquette, V. & Bensimon, D. (2000). Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature 404, 901–4.
Svoboda, K. & Block, S. M. (1994). Biological applications of optical forces. Annu. Rev. Biophys. Biomol. Struct. 23, 247–85.
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.
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.
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.
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.
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.
van Loenhout, M. T., de Grunt, M. V. & Dekker, C. (2012). Dynamics of DNA supercoils. Science 338, 338–94.
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.
Vologodskaia, M. & Vologodskii, A. (2002). Contribution of the intrinsic curvature to measured DNA persistence length. J. Mol. Biol. 317, 205–13.
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.
Vologodskii, A. (2012). Bridged DNA circles: a new model system to study DNA topology. Macromolecules 45, 45–4333.
Vologodskii, A. & Frank-Kamenetskii, M. (2013). Strong bending of the DNA double helix. Nucleic Acids Res. 41, 6785–92.
Vologodskii, A. & Rybenkov, V. V. (2009). Simulation of DNA catenanes. Phys. Chem. Chem. Phys. 11, 10543–52.
Vologodskii, A. V. (1994). DNA extension under the action of an external force. Macromolecules 27, 27–5623.
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.
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.
Vologodskii, A. V. & Cozzarelli, N. R. (1995). Modeling of long-range electrostatic interactions in DNA. Biopolymers 35, 289–96.
Vologodskii, A. V., Lukashin, A. V. & Frank-Kamenetskii, M. D. (1975). Topological interaction between polymer chains. Sov. Phys. JETP 40, 932–6.
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.
Vologodskii, A. V. & Marko, J. F. (1997). Extension of torsionally stressed DNA by external force. Biophys. J. 73, 123–32.
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.
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.
Wang, J. C. (1979). Helical repeat of DNA in solution. Proc. Natl. Acad. Sci. U. S. A. 76, 200–3.
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.
Wang, J. C. (1968). Cyclization of phage DNAs. Cold Spring Harbor Symp. Quant. Biol. 33, 409–15.
Wang, M. D., Yin, H., Landick, R., Gelles, J. & Block, S. M. (1997). Stretching DNA with optical tweezers. Biophys. J. 72, 1335–46.
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.
Watson, J. D. & Crick, F. H. C. (1953). The structure of DNA. Nature 171, 123–31.
Widom, J. & Baldwin, R. L. (1980). Cation-induced toroidal condensation of DNA – studies with Co3+(NH3)6. J. Mol. Biol. 144, 431–53.
Wiggins, P. A., Phillips, R. & Nelson, P. C. (2005). Exact theory of kinkable elastic polymers. Phys. Rev.E 71, 021909.
Williams, M. C., Rouzina, I. & Bloomfield, V. A. (2002). Thermodynamics of DNA interactions from single molecule stretching experiments. Acc. Chem. Res. 35, 159–66.
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.
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.
Yan, J. & Marko, J. F. (2004). Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93, 108108.
Yin, H., Wang, M. D., Svoboda, K., Landick, R., Block, S. M. & Gelles, J. (1995). Transcription against an applied force. Science 270, 1653–7.
Yoo, J. & Aksimentiev, A. (2012). Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations. J. Phys. Chem. B 116, 12946–54.
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.
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.
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.
Zhurkin, V. B., Lysov, Y. P. & Ivanov, V. I. (1979). Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res. 6, 1081–96.