Abstract
The physical aspects of DNA structure and function are overviewed. Major DNA structures are described, which include: the canonical Watson-Crick double helix (B form), B’, A, Z duplex forms, parallel-stranded DNA, triplexes and quadruplexes. Theoretical models, which are used to treat DNA, are considered with special emphasis on the elastic-rod model. DNA topology, supercoiling and their biological signi.cance are extensively discussed. Recent developments in the understanding of molecular interactions responsible for the stability of the DNA double helix are presented.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Anshelevich, V.V., Vologodskii, A.V., Lukashin, A.V., Frank-Kamenetskii, M.D., 1979. Statistical-mechanical treatment of violations of the double helix in supercoiled DNA. Biopolymers 18: 2733–2744.
Anshelevich, V.V., Vologodskii, A.V., Lukashin, A.V., Frank-Kamenetskii, M.D., 1984. Slow relaxational processes in the melting of linear biopolymers. A theory and its application to nucleic acids. Biopolymers 23: 39–58.
Anshelevich, V.V., Vologodskii, A.V., Frank-Kamenetskii, M.D., 1988. A theoretical study of formation of DNA noncanonical structures under negative superhelical stress. J. Biomol. Struct. Dyn. 6: 247–259.
Azbel', M.Y., 1972. The inverse problem for DNA. JETP Lett. 16: 128–131.
Berger, J.M., Gamblin, S.J., Harrison, S.C.,Wang, J.C., 1996. Structure and mechanism of DNA topoisomerase II. Nature 379: 225–232.
Breslauer, K.J., Freire, E., Straume, M., 1992. Calorimetry: a tool for DNA and ligand-DNA studies. Methods Enzymol. 211: 533–567.
Bustamante, C., Marko, J.F., Siggia, E.D., Smith, S., 1994. Entropic elasticity of lambdaphage DNA. Science 265: 1599–1600.
Bustamante, C., Bryant, Z., Smith, S.B. 2003. Ten years of tension: single-molecule DNA mechanics. Nature 421: 423–427.
Chan, S.R., Blackburn, E.H. 2004. Telomeres and telomerase. Philos. Trans. R. Soc. Lond. B Biol Sci. 359: 109–121.
Chen, L., Cai, L., Zhang, X., Rich, A., 1994. Crystal structure of a four-stranded intercalated DNA: d(C4). Biochemistry 33: 13540–13546.
Depew, R.E., Wang, J.C., 1975. Conformational fiuctuations of DNA helix. Proc. Natl. Acad. Sci. USA, 72: 4275–4279.
Deruchi, T., Tsurusaki, K., 1993a. A new algorithm for numerical calculation of link invariants. Phys. Lett. A 174: 29–37.
Deruchi, T., Tsurusaki, K., 1993b. Topology of closed random polygons. J. Phys. Soc. Japan 62: 1411–1414.
Deruchi, T., Tsurusaki, K., 1994. A statistical study of random knotting using the Vassiliev invariants. J. Knot Theory and Its Ramifications 3: 321–353.
Dickerson, R.E., 1992. DNA structure from A to Z. Methods Enzymol. 211: 67–111.
Du, Q., M. Vologodskaia, H. Kuhn, M. Frank-Kamenetskii and A. Vologodskii, 2005. Gapped DNA and cyclization of short DNA fragments, Biophys. J. 88: 4137–4145.
Epel, E.S., Blackburn, E.H., Lin, J., Dhabhar, F.S., Adler, NE, Morrow, J.D., Cawthon, R.M. 2004. Accelerated telomere shortening in response to life stress. Proc. Natl. Acad. Sci. USA 101: 17312–17315.
Fixman, M., Freire, J.J., 1977. Theory of DNA melting curves. Biopolymers 16: 2693–2704.
Frank-Kamenetskii, M.D., 1997. Unraveling DNA. The Most Important Molecule of Life. Addison Wesley, Reading, MA.
Frank-Kamenetskii, M.D., Frank-Kamenetskii, A.D., 1969. Theory of helix-coil transition for the case of double stranded DNA. Molek. Biol. 3: 375–382.
Frank-Kamenetskii, M.D., Lukashin, A.V., Vologodskii, A.V., 1975. Statistical mechanics and topology of polymer chains. Nature 258: 398–399.
Frank-Kamenetskii, M.D., Lukashin, A.V., Anshelevich, V.V., Vologodskii, A.V., 1985. Topsional and bending rigidity of the double helix from data on small DNA rings. J. Biomol. Struct. Dyn. 2: 1005–1012.
Frank-Kamenetskii, M.D., Mirkin, S.M., 1995. Triplex DNA structures. Ann. Rev. Biochem. 64: 65–95.
Frank-Kamenetskii, M.D., Vologodskii, A.V., 1981. Topological aspects of polymer physics: theory and its biophysical applications. Sov. Phys. Usp. 24: 679–696.
Frank-Kamenetskii, M.D., Vologodskii, A.V., 1984. Thermodynamics of the B-Z transition in superhelical DNA. Nature 307: 481–482.
Frisch, H.L., 1993. Macromolecular topology. Metastable isomers from pseudo interpenetrating polymer networks. New J. Chem. 17: 697–701.
Fuller, F.B., 1971. The writhing number of a space curve. Proc. Natl. Acad. Sci. USA 68: 815–819.
Gehring, K., Leroy, J.L. Gueron, M., 1993. A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature 363: 561–565.
Gotoh, O., Tagashira, Y., 1981. Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers 20: 1033–1042.
Grosberg, A.I., Khokhlov, A.R., 1994. Statistical Physics of Macromolecules. AIP Press, New York.
Hagerman, P.J., 1988. Flexibility of DNA, Ann. Rev. Biophys. Biophys. Chem. 17: 265–286.
Harris, S.A., Sands, Z.A., and Laughton, C.A., 2005. Molecular dynamics Simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys. J. 88: 1684–1691.
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.
Ivanov, V.I., Krylov, D.Y., 1992. A-DNA in solution as studied by diverse approaches. Methods Enzymol. 211: 111–127.
Kalambet, Y.A., Borovik, A.S., Lyamichev, V.I., Lyubchenko, Y.L., 1985. Electron microscopy of the melting of sequenced DNA. Biopolymers 24: 359–377.
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: 1173–1185.
Klenin, K.V., Vologodskii, A.V., Anshelevich, V.V., Dykhne, A.M., Frank-Kamenetskii, M.D., 1991. Computer stimulation of DNA supercoiling. J. Mol. Biol. 217: 413–419.
Kozyavkin, S.A., Lyubchenko, Y.L., 1984. The nonequilibrium character of DNA melting: effects of heating rate on the fine structure of melting curves. Nucl. Acids Res. 12: 4339–4349.
Kozyavkin, S.A. Naritsin, D.B., Lyubchenko, Y.L., 1986. The kinetics of DNA helix-coil subtransitions. J. Biomol. Struct. Dyn. 3: 689–704.
Lifshitz, I.M., 1973. On the statistical thermodynamics of fusion of long heteropolymer chains. Sov. Phys.-JETP 65: 1100–1110.
Liu, L., Depew, R.E.,Wang, J.C., 1976. Knotted single-stranded DNA rings: a novel topological isomer of circular single-stranded DNA formed by treatment with Escherichia coli w protein. J. Mol. Biol. 106: 439–452.
Lukashin, A.V., Vologodskii, A.V., Frank-Kamenetskii, M.D., 1976. Comparison of different theoretical descriptions of helix-coil transition in DNA. Biopolymers 15: 1841–1844.
Lyamichev, V.I., Mirkin, S.M., Frank-Kamenetskii, M.D., 1985. A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J. Biomol. Struct. Dyn. 3: 327–338.
Lyamichev, V.I., Mirkin, S.M., Frank-Kamenetskii, M.D., 1986. Structures of homopurine-homopyrimidine tract in superhelical DNA. J. Biomol. Struct. Dyn. 3: 667–669.
Lyamichev, V.I., Mirkin, S.M., Frank-Kamenetskii, M.D., Cantor, C.R., 1988. A stable complex between homopyrimidine oligomers and the homologous regions of duplex DNA. Nucl. Acids Res. 16: 2165–2178.
Lyubchenko, Y.L., Vologodskii, A.V., Frank-Kamenetskii, M.D., 1978. Direct comparison of theoretical and experimental melting profiles for φX174 DNA. Nature 271: 28–31.
Marko, J.F., Siggia, E.D., 1994. Fluctuations and supercoiling of DNA. Science 265: 506–508.
Marko, J.F., Siggia, E.D., 1995. Statistical mechanics of supercoiled DNA. Phys. Rev. E 52: 2912–2938.
Marmur, J., Doty, P., 1962. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 5: 109–118.
Matzke, M.A., Birchler, J.A. 2005. RNAi-mediated pathways in the nucleus. Nat Rev Genet. 6: 24–35.
Mirkin, S.M., Lyamichev, V.I., Drushlyak, K.N., Dobrynin, V.N., Filippov, S.A., Frank-Kamenetskii, M.D., 1987. DNA H form requires a homopurine-homopyrimidine mirror repeat. Nature 330: 495–497.
Mirkin, S.M., Frank-Kamenetskii, M.D., 1994. H-DNA and related structures. Ann. Rev. Biophys. Biomol. Struct. 23: 541–576.
Moser, H.E., Dervan, P.B., 1987. Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238: 645–650.
Novina, C.D., Sharp, P.A. 2004. The RNAi revolution. Nature 430: 161–164.
Poland, D., 1974. Recursion relation generation of probability profiles for specificsequence macromolecules with long-range correlations. Biopolymers 13: 1859–1871.
Protozanova E., Yakovchuk, P., Frank-Kamenetskii, M.D. 2004. Stacked-unstacked equilibrium at the Nick site of DNA. J.Mol.Boil. 342: 775–785.
Pulleyblank, D.E., Shure, D.E., Tang, D., Vinograd, J., Vosberg, H.-P. 1975. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc. Natl. Acad. Sci. USA 72: 4280–4284.
Rippe, K., Jovin, T.M., 1992. Parallel-stranded Duplex DNA. Methods Enzymol. 211: 199–220.
Rouzina, I., Bloom.eld, V.A. 2001a. Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys J. 80: 882–293.
Rouzina, I., Bloom.eld, V.A. 2001b. Force-induced melting of the DNA double helix 2. Effect of solution conditions. Biophys J. 80: 894–900.
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. USA 90: 5307–5311.
Rybenkov, V.V., Ullsperger C, Vologodskii, A.V., Cozzarelli, N.R. 1997. Simplication of DNA topology below equilibrium values by type II topoisomerases. Science 277: 690–693.
SantaLucia, J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95: 1460–1465.
Selinger, J.V., Selinger, R.L.B., 1996. Theory of chiral order in random copolymers. Phys. Rev. Lett. 76: 58–61.
Shaw, S.Y., Wang, J.C., 1993. Knotting of a DNA chain during ring closure, Science 260: 533–536.
Sinden, R.R., 1994. DNA Structure and Function. Academic Press, San Diego.
Smith, S.B., Finzi, L., Bustamante, C., 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258: 1122–1126.
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: 795–789.
Soyfer, V.N., Potaman, V.V., 1996. Triple-helical Nucleic Acids. Springer, New York.
Stigter, D., 1977. Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers 16: 1435–1448.
Strick, T.R., Allemand, J.F., Bensimon, D., Bensimon, A., Croquette, V., 1996. The elasticity of a single supercoiled DNA molecule. Science 271: 1835–1837.
Taylor, W.H., Hagerman, P.J., 1990. Application of the method of phage T4 DNA ligasecatalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA fiexibility and helical repeat. J. Mol. Biol. 212: 363–376.
Vedenov, A.A., Dykhne, A.M., Frank-Kamenetskii, A.D., Frank-Kamenetskii, M.D., 1967. A contribution to the theory of helix-coil transition in DNA. Molek. Biol. 1: 313–319.
Vedenov, A.A., Dykhne, A.M., Frank-Kamenetskii, M.D., 1971. The helix-coil transition in DNA. Sov. Phys. Usp. 14: 715–736.
Vologodskaia, M. and A. Vologodskii. 2002. Contribution of the intrinsic curvature to measured DNA persistence length. J. Mol. Biol. 317: 205–213.
Vologodskii, A.V., Lukashin, A.V., Frank-Kamenetskii, M.D., Anshelevich, V.V., 1974. The knot problem in statistical mechanics of polymer chains. Sov. Phys. JETP 39: 1059–1063.
Vologodskii, A.V., Lukashin, A.V., Anshelevich, V.V., Frank-Kamenetskii, M.D., 1979b. Fluctuations in superhelical DNA. Nucleic Acids Res. 6: 967–982.
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: 131–148.
Vologodskii, A.V., Frank-Kamenetskii, M.D., 1982. Theoretical study of cruciform states in superhelical DNA. FEES Lett. 143: 257–260.
Vologodskii, A.V., Frank-Kamenetskii, 1984. Left-handed Z form in superhelical DNA: a theoretical study. J. Biomol. Struct. Dyn. 1: 1325–1333.
Vologodskii, A.V., Frank-Kamenetskii, M.D., 1992 Modeling DNA supercoiling. Methods Enzymol. 211, 467–480
Vologodskii, A.V., Levene, S.D., Klenin, K.V., Frank-Kamenetskii, M.D., Cozzarelli, N.R., 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227: 1224–1243.
Vologodskii, A.V., Zhang, W., Rybenkov, V.V., Podtelezhnikov, A.A., Subramanian, D., Grif.th, J.D., Cozzarelli, N.R. 2001. Mechanism of topology simplification by type II DNA topoisomerases. Proc. Natl. Acad. Sci. USA. 98: 3045–3049.
Wada, A., Suyama, A., 1986. Local stability of DNA and RNA secondary structure and its relation to biological functions. Prog. Biophys. Mol. Biol. 47: 113–157.
Wada, A., Yabuki, S., Husimi, Y., 1980. Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies. CRC Crit. Rev. Biochem. 9: 87–144.
Wang, J.C., 1996. DNA topoisomerase. Annu. Rev. Biochem. 65: 635–692.
Wang, A.H.-J., Quigley, G.J., Kolpak, F.K., 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: 680–685.
Wartell, R.M., Benight, A.S., 1985. Thermal denaturation of DNA molecules: a comparison of theory with experiment. Phys. Rep. 126: 67–107.
Watson, J.D., Crick, F.H.C. 1953. Molecular structure of nucleic acids. Nature 171: 737–738.
White, J.H., 1969. Self-linking and the Gauss integral in higher dimensions. Am. J. Math. 91: 693–728.
Williams, M.C., Rouzina, I. 2002. Force spectroscopy of single DNA and RNA molecules. Curr. Opin. Struct. Biol. 12: 330–336.
Williams, M.C., Rouzina, I., Bloom.eld, V.A. 2002. Thermodynamics of DNA interactions from single molecule stretching experiments. Acc. Chem. Res. 35: 159–166.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer
About this paper
Cite this paper
Frank-Kamenetskii, M.D. (2006). PHYSICS OF DNA. In: Golovin, A.A., Nepomnyashchy, A.A. (eds) Advances in Sensing with Security Applications. NATO Science Series II: Mathematics, Physics and Chemistry, vol 218. Springer, Dordrecht. https://doi.org/10.1007/1-4020-4355-4_10
Download citation
DOI: https://doi.org/10.1007/1-4020-4355-4_10
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-4354-3
Online ISBN: 978-1-4020-4355-0
eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)