Skip to main content

Part of the book series: NATO Science Series II: Mathematics, Physics and Chemistry ((NAII,volume 218))

  • 693 Accesses

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 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.

    Article  Google Scholar 

  2. 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.

    Article  Google Scholar 

  3. 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.

    Google Scholar 

  4. Azbel', M.Y., 1972. The inverse problem for DNA. JETP Lett. 16: 128–131.

    ADS  Google Scholar 

  5. Berger, J.M., Gamblin, S.J., Harrison, S.C.,Wang, J.C., 1996. Structure and mechanism of DNA topoisomerase II. Nature 379: 225–232.

    Article  ADS  Google Scholar 

  6. Breslauer, K.J., Freire, E., Straume, M., 1992. Calorimetry: a tool for DNA and ligand-DNA studies. Methods Enzymol. 211: 533–567.

    Article  Google Scholar 

  7. Bustamante, C., Marko, J.F., Siggia, E.D., Smith, S., 1994. Entropic elasticity of lambdaphage DNA. Science 265: 1599–1600.

    Article  ADS  Google Scholar 

  8. Bustamante, C., Bryant, Z., Smith, S.B. 2003. Ten years of tension: single-molecule DNA mechanics. Nature 421: 423–427.

    Article  ADS  Google Scholar 

  9. Chan, S.R., Blackburn, E.H. 2004. Telomeres and telomerase. Philos. Trans. R. Soc. Lond. B Biol Sci. 359: 109–121.

    Article  Google Scholar 

  10. Chen, L., Cai, L., Zhang, X., Rich, A., 1994. Crystal structure of a four-stranded intercalated DNA: d(C4). Biochemistry 33: 13540–13546.

    Article  Google Scholar 

  11. Depew, R.E., Wang, J.C., 1975. Conformational fiuctuations of DNA helix. Proc. Natl. Acad. Sci. USA, 72: 4275–4279.

    Article  ADS  Google Scholar 

  12. Deruchi, T., Tsurusaki, K., 1993a. A new algorithm for numerical calculation of link invariants. Phys. Lett. A 174: 29–37.

    Article  ADS  Google Scholar 

  13. Deruchi, T., Tsurusaki, K., 1993b. Topology of closed random polygons. J. Phys. Soc. Japan 62: 1411–1414.

    Article  ADS  Google Scholar 

  14. Deruchi, T., Tsurusaki, K., 1994. A statistical study of random knotting using the Vassiliev invariants. J. Knot Theory and Its Ramifications 3: 321–353.

    Article  Google Scholar 

  15. Dickerson, R.E., 1992. DNA structure from A to Z. Methods Enzymol. 211: 67–111.

    Article  Google Scholar 

  16. 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.

    Article  Google Scholar 

  17. 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.

    Article  ADS  Google Scholar 

  18. Fixman, M., Freire, J.J., 1977. Theory of DNA melting curves. Biopolymers 16: 2693–2704.

    Article  Google Scholar 

  19. Frank-Kamenetskii, M.D., 1997. Unraveling DNA. The Most Important Molecule of Life. Addison Wesley, Reading, MA.

    Google Scholar 

  20. 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.

    Google Scholar 

  21. Frank-Kamenetskii, M.D., Lukashin, A.V., Vologodskii, A.V., 1975. Statistical mechanics and topology of polymer chains. Nature 258: 398–399.

    Article  ADS  Google Scholar 

  22. 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.

    Google Scholar 

  23. Frank-Kamenetskii, M.D., Mirkin, S.M., 1995. Triplex DNA structures. Ann. Rev. Biochem. 64: 65–95.

    Article  Google Scholar 

  24. Frank-Kamenetskii, M.D., Vologodskii, A.V., 1981. Topological aspects of polymer physics: theory and its biophysical applications. Sov. Phys. Usp. 24: 679–696.

    Article  ADS  Google Scholar 

  25. Frank-Kamenetskii, M.D., Vologodskii, A.V., 1984. Thermodynamics of the B-Z transition in superhelical DNA. Nature 307: 481–482.

    Article  ADS  Google Scholar 

  26. Frisch, H.L., 1993. Macromolecular topology. Metastable isomers from pseudo interpenetrating polymer networks. New J. Chem. 17: 697–701.

    Google Scholar 

  27. Fuller, F.B., 1971. The writhing number of a space curve. Proc. Natl. Acad. Sci. USA 68: 815–819.

    Article  MathSciNet  MATH  ADS  Google Scholar 

  28. Gehring, K., Leroy, J.L. Gueron, M., 1993. A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature 363: 561–565.

    Article  ADS  Google Scholar 

  29. 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.

    Article  Google Scholar 

  30. Grosberg, A.I., Khokhlov, A.R., 1994. Statistical Physics of Macromolecules. AIP Press, New York.

    Google Scholar 

  31. Hagerman, P.J., 1988. Flexibility of DNA, Ann. Rev. Biophys. Biophys. Chem. 17: 265–286.

    Article  Google Scholar 

  32. 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.

    Article  Google Scholar 

  33. 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.

    Article  Google Scholar 

  34. Ivanov, V.I., Krylov, D.Y., 1992. A-DNA in solution as studied by diverse approaches. Methods Enzymol. 211: 111–127.

    Article  Google Scholar 

  35. 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.

    Article  Google Scholar 

  36. 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.

    Google Scholar 

  37. 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.

    Article  Google Scholar 

  38. 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.

    Article  Google Scholar 

  39. Kozyavkin, S.A. Naritsin, D.B., Lyubchenko, Y.L., 1986. The kinetics of DNA helix-coil subtransitions. J. Biomol. Struct. Dyn. 3: 689–704.

    Google Scholar 

  40. Lifshitz, I.M., 1973. On the statistical thermodynamics of fusion of long heteropolymer chains. Sov. Phys.-JETP 65: 1100–1110.

    Google Scholar 

  41. 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.

    Article  Google Scholar 

  42. 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.

    Article  Google Scholar 

  43. 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.

    Google Scholar 

  44. 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.

    Google Scholar 

  45. 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.

    Article  Google Scholar 

  46. 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.

    Article  ADS  Google Scholar 

  47. Marko, J.F., Siggia, E.D., 1994. Fluctuations and supercoiling of DNA. Science 265: 506–508.

    Article  ADS  Google Scholar 

  48. Marko, J.F., Siggia, E.D., 1995. Statistical mechanics of supercoiled DNA. Phys. Rev. E 52: 2912–2938.

    Article  MathSciNet  ADS  Google Scholar 

  49. Marmur, J., Doty, P., 1962. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 5: 109–118.

    Article  Google Scholar 

  50. Matzke, M.A., Birchler, J.A. 2005. RNAi-mediated pathways in the nucleus. Nat Rev Genet. 6: 24–35.

    Article  Google Scholar 

  51. 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.

    Article  ADS  Google Scholar 

  52. Mirkin, S.M., Frank-Kamenetskii, M.D., 1994. H-DNA and related structures. Ann. Rev. Biophys. Biomol. Struct. 23: 541–576.

    Article  Google Scholar 

  53. Moser, H.E., Dervan, P.B., 1987. Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238: 645–650.

    Article  ADS  Google Scholar 

  54. Novina, C.D., Sharp, P.A. 2004. The RNAi revolution. Nature 430: 161–164.

    Article  ADS  Google Scholar 

  55. Poland, D., 1974. Recursion relation generation of probability profiles for specificsequence macromolecules with long-range correlations. Biopolymers 13: 1859–1871.

    Article  Google Scholar 

  56. Protozanova E., Yakovchuk, P., Frank-Kamenetskii, M.D. 2004. Stacked-unstacked equilibrium at the Nick site of DNA. J.Mol.Boil. 342: 775–785.

    Article  Google Scholar 

  57. 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.

    Article  ADS  Google Scholar 

  58. Rippe, K., Jovin, T.M., 1992. Parallel-stranded Duplex DNA. Methods Enzymol. 211: 199–220.

    Article  Google Scholar 

  59. Rouzina, I., Bloom.eld, V.A. 2001a. Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys J. 80: 882–293.

    Google Scholar 

  60. 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.

    Article  Google Scholar 

  61. 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.

    Article  ADS  Google Scholar 

  62. 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.

    Article  Google Scholar 

  63. SantaLucia, J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95: 1460–1465.

    Article  ADS  Google Scholar 

  64. Selinger, J.V., Selinger, R.L.B., 1996. Theory of chiral order in random copolymers. Phys. Rev. Lett. 76: 58–61.

    Article  ADS  Google Scholar 

  65. Shaw, S.Y., Wang, J.C., 1993. Knotting of a DNA chain during ring closure, Science 260: 533–536.

    Article  ADS  Google Scholar 

  66. Sinden, R.R., 1994. DNA Structure and Function. Academic Press, San Diego.

    Google Scholar 

  67. 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.

    Article  ADS  Google Scholar 

  68. 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.

    Article  ADS  Google Scholar 

  69. Soyfer, V.N., Potaman, V.V., 1996. Triple-helical Nucleic Acids. Springer, New York.

    Google Scholar 

  70. Stigter, D., 1977. Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers 16: 1435–1448.

    Article  Google Scholar 

  71. 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.

    Article  ADS  Google Scholar 

  72. 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.

    Article  Google Scholar 

  73. 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.

    Google Scholar 

  74. Vedenov, A.A., Dykhne, A.M., Frank-Kamenetskii, M.D., 1971. The helix-coil transition in DNA. Sov. Phys. Usp. 14: 715–736.

    Article  ADS  Google Scholar 

  75. Vologodskaia, M. and A. Vologodskii. 2002. Contribution of the intrinsic curvature to measured DNA persistence length. J. Mol. Biol. 317: 205–213.

    Article  Google Scholar 

  76. 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.

    MathSciNet  ADS  Google Scholar 

  77. Vologodskii, A.V., Lukashin, A.V., Anshelevich, V.V., Frank-Kamenetskii, M.D., 1979b. Fluctuations in superhelical DNA. Nucleic Acids Res. 6: 967–982.

    Article  Google Scholar 

  78. 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.

    Google Scholar 

  79. Vologodskii, A.V., Frank-Kamenetskii, M.D., 1982. Theoretical study of cruciform states in superhelical DNA. FEES Lett. 143: 257–260.

    Article  Google Scholar 

  80. Vologodskii, A.V., Frank-Kamenetskii, 1984. Left-handed Z form in superhelical DNA: a theoretical study. J. Biomol. Struct. Dyn. 1: 1325–1333.

    Google Scholar 

  81. Vologodskii, A.V., Frank-Kamenetskii, M.D., 1992 Modeling DNA supercoiling. Methods Enzymol. 211, 467–480

    Article  Google Scholar 

  82. 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.

    Article  Google Scholar 

  83. 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.

    Article  ADS  Google Scholar 

  84. 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.

    Article  Google Scholar 

  85. 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.

    Article  Google Scholar 

  86. Wang, J.C., 1996. DNA topoisomerase. Annu. Rev. Biochem. 65: 635–692.

    Article  Google Scholar 

  87. 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.

    Article  ADS  Google Scholar 

  88. Wartell, R.M., Benight, A.S., 1985. Thermal denaturation of DNA molecules: a comparison of theory with experiment. Phys. Rep. 126: 67–107.

    Article  ADS  Google Scholar 

  89. Watson, J.D., Crick, F.H.C. 1953. Molecular structure of nucleic acids. Nature 171: 737–738.

    Article  ADS  Google Scholar 

  90. White, J.H., 1969. Self-linking and the Gauss integral in higher dimensions. Am. J. Math. 91: 693–728.

    Article  MATH  Google Scholar 

  91. Williams, M.C., Rouzina, I. 2002. Force spectroscopy of single DNA and RNA molecules. Curr. Opin. Struct. Biol. 12: 330–336.

    Article  Google Scholar 

  92. 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.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints 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

Publish with us

Policies and ethics