Conformational Peculiarities and Biological Role of Some Nucleotide Sequences

  • V. I. Poltev
  • A. V. Teplukhin
  • V. P. Chuprina


A conclusion about the dependence of the conformational behavior of nucleic acids on nucleotide sequences has been made on the basis of nonbonded interaction energy calculations using the classical potential functions. The potential functions have been chosen by comparing the results of calculations for model systems (crystals, associates) with the experimental data and with the results of the most rigorous quantum mechanical calculations. Potentials proposed by other authors and the possibilities of further refinement of potential functions are considered.

To study conformational patterns of different nucleotide sequences we have calculated the energy of interaction between base pairs (all combinations have been considered) as a function of the parameters determining their mutual position in the double helix. The calculations have shown, in accordance with the experimental data, that there are sequences for which the energy preferred conformations are the A-like ones (e. g. GG, AT, AC) while for other sequences the preferred conformations are the B-like ones (e. g. AA, TA, CA).

Theoretical conformational analysis of a regular double-helical polynucleotide has shown the existence of two regions of minimal energy values corresponding to the A- and B-families of nucleic acid conformations. Taking into account the possible biological role of sequences containing repeating adenines in one chain and repeating thymines in the other one, we have considered other possible regular conformations of poly(dA) • poly(dT). Two more regions of minimal energy values have been revealed which correspond to the A-like conformation of one chain and the B-like conformation of the other one. The relative energetic advantages of the four regions depends on phosphate group charge neutralization.


Double Helix Mutual Position Nonbonded Interaction Conformational Parameter Helix Axis 
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  1. 1.
    R.E. Dickerson, M.L. Kopka and H.R. Drew, Structural correlations in B-DNA, in “Structure and Dynamics: Nucleic Acids and Proteins,” E. Clementi and R.H. Sarma, eds., Adenine Press, N.Y., p. 149 (1983).Google Scholar
  2. 2.
    R.E. Dickerson, M.L. Kopka and P. Pjura, Base sequence, helix geometry, hydration and helix stability in B-DNA, in “Biological Macromolecules and Assemblies,” F.A. Jurnak and A. McPherson, eds., Wiley, N.Y., 237 (1985).Google Scholar
  3. 3.
    Z. Shakked and O. Kennard, The A form of DNA, ibid., 1.Google Scholar
  4. 4.
    A.H.-J. Wang and A. Rich, The structure of the Z form of DNA, ibid., 127.Google Scholar
  5. 5.
    D.J. Patel, S.A. Kozlowski and R. Bhatt, Sequence dependence of base-pair stacking in right-handed DNA in solution: Proton nuclear Overhauser effect NMR measurements, Proc. Natl. Acad. Sci. USA, 80, 3908 (1983).PubMedCrossRefGoogle Scholar
  6. 6.
    G.M. Clore and A.M. Gronenborn, Interproton distance measurements in solution for a double-stranded DNA undecamer comprising a portion of the specific target site for cyclic AMP receptor protein in the gal operon. A nuclear Overhauser enhancement study, FEBS Lett., 175, 117 (1984).PubMedCrossRefGoogle Scholar
  7. 7.
    C.R. Calladine, Mechanics of sequence-dependent stacking of bases in B-DNA, J. Mol. Biol., 161, 343 (1982).PubMedCrossRefGoogle Scholar
  8. 8.
    R.E. Dickerson, Base sequence and helix structure variation in B and A DNA, J. Mol. Biol., 166, 414 (1983).CrossRefGoogle Scholar
  9. 9.
    C.R. Calladine and H.R. Drew, A base-centered explanation of the B-to-A transition in DNA, J. Mol. Biol., 178, 773 (1984).PubMedCrossRefGoogle Scholar
  10. 10.
    V.I. Poltev and V.P. Chuprina, Relation of macromolecular structure and dynamics of DNA to the mechanisms of fidelity and errors of nucleic acid biosynthesis, in “Structure and Motion: Membranes, Nucleic Acids and Proteins,” E. Clementi et al., eds., Adenine Press, N.Y., 433 (1985).Google Scholar
  11. 11.
    V.I. Poltev, Simulation of intermolecular and intramolecular interactions of nucleic acid subunits by means of atom-atom potential functions, Int. J. Quantum Chem., 16, 863 (1979).CrossRefGoogle Scholar
  12. 12.
    V.B. Zhurkin, V.I. Poltev and V.L. Florentiev, Atom-atom potential functions for conformational analysis of nucleic acids, Mol. Biol. USSR, 14, 1116 (1980).Google Scholar
  13. 13.
    V.I. Poltev and N.V. Shulyupina, Stimulation of interactions between nucleic acid bases by refined atom-atom potential functions, J. Biomol. Struct. Dyn., 3, 739 (1986).PubMedCrossRefGoogle Scholar
  14. 14.
    V.I. Poltev, T.I. Grokhlina and G.G. Malenkov, Hydration of nucleic acid bases studied using novel atom-atom potential functions, J. Biomol. Struct. Dyn., 2, 413 (1984).PubMedCrossRefGoogle Scholar
  15. 15.
    F.A. Momany, L.M. Carruthers, R.F. McGuire and H.A. Scheraga, Intermolecular potentials from crystal data. 3. Determination of empirical potentials and application to the packing conformation and lattice energies in crystals of hydrocarbons, carboxylic acids, amines and amindes, J. Phys. Chem., 78, 1595 (1974).CrossRefGoogle Scholar
  16. 16.
    S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Singh, C. Chio, G. Alagona, S. Profeta and P. Weiner, A new force field for molecular mechanical simulation of nucleic acids and proteins, J. Amer. Chem. Soc., 106, 765 (1984).CrossRefGoogle Scholar
  17. 17.
    R. Scordamaglia, F. Cavallone and E. Clementi, Analytical potentials from ab initio computations for the interaction between biomolecules. 2. Water with the four bases of DNA, J. Amer. Chem. Soc, 99, 5545 (1977).CrossRefGoogle Scholar
  18. 18.
    O. Matsuoka, C. Tosi and E. Clementi, Conformational studies on polynucleotide chains. 1. Hartree-Fock energies and description of nonbonded interactions with Lennard-Jones potentials, Biopolymers, 17, 33 (1978).PubMedCrossRefGoogle Scholar
  19. 19.
    H. Berthod and A. Pullman, Sur le calcul des caracteristiques de la squelette des molecules conjuguees, J. Chim. Phys., 62, 942 (1965).Google Scholar
  20. 20.
    R. Lavery, K. Zakrzewska and A. Pullman, Optimized monopole expansions for the representation of the electrostatic properties of the nucleic acids, J. Comput. Chem., 5, 363 (1984).CrossRefGoogle Scholar
  21. 21.
    N.K. Ray, M. Shibata, G. Bolis and R. Rein, Potential-derived point-charge model study of electrostatic interactions in DNA base components, Chem. Phys. Lett., 109, 352 (1984).PubMedCrossRefGoogle Scholar
  22. 22.
    H. DeVoe and I. Tinoco, The stability of helical polynucleotides: Base contributions, J. Mol. Biol., 4, 500 (1962).PubMedCrossRefGoogle Scholar
  23. 23.
    V.I. Ponomaryov, O.S. Filipenko and L.O. Atovmyan, Crystal and molecular structure of naphthalene at — 150°C, Krystallografia USSR, 21, 393 (1976).Google Scholar
  24. 24.
    R.S. Bradley, T.G. Cleasby, The vapour pressure and lattice energy of some aromatic ring compounds, J. Chem. Soc., 6, 1690 (1953).CrossRefGoogle Scholar
  25. 25.
    R. Mason, The crystallography of antracene at 95 K and 290 K, Acta Cryst., 17, 547 (1964).CrossRefGoogle Scholar
  26. 26.
    J.D. Kelley and F.O. Rice, The vapour pressures of some polynuclear aromatic hydrocarbons, J. Phys. Chem., 68, 3794 (1964).CrossRefGoogle Scholar
  27. 27.
    A. Camerman and J. Trotter, The crystal and molecular structure of pyrene, Acta Cryst., 18, 636 (1965).CrossRefGoogle Scholar
  28. 28.
    P.J. Wheatley, The crystal and molecular structure of pyrazine, Acta Cryst., 10, 182 (1957).CrossRefGoogle Scholar
  29. 29.
    J. Tjebbes, The heats of combustion and formation of the three diazines and their resonance energies, Acta Chem. Scand., 16, 916 (1962).CrossRefGoogle Scholar
  30. 30.
    P.J. Wheatley, The crystal and molecular structure of pyrimidine, Acta Cryst., 13, 80 (1960).CrossRefGoogle Scholar
  31. 31.
    J. Trotter, A three-dimensional analysis of the crystal structure of p-benzoquinone, Acta Cryst., 13, 86 (1960).CrossRefGoogle Scholar
  32. 32.
    A.S. Coolidge and M.S. Coolidge, The sublimation pressures of substituted quinones and hydroquinones, J. Amer. Chem. Soc, 49, 100 (1927).CrossRefGoogle Scholar
  33. 33.
    W. Bolton, The crystal structure of alloxan, Acta Cryst., 17, 147 (1964).CrossRefGoogle Scholar
  34. 34.
    S. Martinez-Carrera, The crystal structure of imidazole at-150°C, Acta Cryst., 20, 783 (1966).CrossRefGoogle Scholar
  35. 35.
    H. Zimmermann and H. Geisenfelder, Uber die Mesomerieenergie von Azolen, Z. Electroch., 65, 368 (1961).Google Scholar
  36. 36.
    R.F. Stewart and L.H. Jensen, Redetermination of the crystal structure of uracil, Acta Cryst., 23, 1102 (1967).CrossRefGoogle Scholar
  37. 37.
    I.K. Yanson, B.I. Verkin, O.I. Shklyarevsky and A.B. Teplitsky, Sublimation heats of nitrogen bases of nucleic acids, Studia Biophys., 46, 29 (1974).Google Scholar
  38. 38.
    D.L. Barker and R.E. Marsh, The crystal structure of cytosine, Acta Cryst., 17, 1581 (1964).CrossRefGoogle Scholar
  39. 39.
    H. Ringertz, The molecular and crystal structure of uric acid, Acta Cryst., 20, 397 (1966).CrossRefGoogle Scholar
  40. 40.
    A.G.W. Leslie, S. Arnott, R. Chandrasekaran and R.L. Ratliff, Polymorphism of DNA double helices, J. Mol. Biol., 143, 49 (1980).PubMedCrossRefGoogle Scholar
  41. 41.
    V.I. Ivanov, V.B. Zhurkin, S.K. Zavriev, Yu. P. Lysov, L.E. Minchenkova, E.E. Minyat, M.D. Frank-Kamenetskii and A.K. Schyolkina, Conformational possibilities of double-helical nucleic acids: Theory and experiment, Int. J. Quant. Chem., 16, 189 (1979).CrossRefGoogle Scholar
  42. 42.
    V.I. Ivanov, Possible relevance of the B-A transition in DNA to transcription, Comments Mol. Cell. Bioph., 2, 333 (1985).Google Scholar
  43. 43.
    G.P. Lomonossoff, P.J.G. Butler and A. Klug, Sequence-dependent variation in the conformation of DNA, J. Mol. Biol., 149, 745 (1981).PubMedCrossRefGoogle Scholar
  44. 44.
    H.R. Drew and A.A. Travers, DNA structural variations in the E. coli tyrT promoter, Cell, 37, 491 (1984).PubMedCrossRefGoogle Scholar
  45. 45.
    V.B. Zhurkin, Yu.P. Lysov and V.I. Ivanov, Different families of double-stranded conformations of DNA as revealed by computer calculations, Biopolymers, 17, 377 (1978).CrossRefGoogle Scholar
  46. 46.
    V.E. Khutorsky and V.I. Poltev, Conformations of double-helical nucleic acids, Nature, 264, 483 (1976).PubMedCrossRefGoogle Scholar
  47. 47.
    V.P. Chuprina, V.E. Khutorsky and V.I. Poltev, Theoretical refinement of A-and B-conformation models of regular polynucleotides, Studia Biophys., 85, 81 (1981).Google Scholar
  48. 48.
    S. Arnott, The geometry of nucleic acids, Progr. Biophys. Mol. Biol., 21, 265 (1970).CrossRefGoogle Scholar
  49. 49.
    V.I. Poltev and A.V. Teplukhin, Interaction of nucleic acid bases and conformational behaviour of repeating nucleotide sequences, Mol. Biol. USSR, 20, No. 6, in press (1986).Google Scholar
  50. 50.
    V.I. Poltev and A.V. Teplukhin, in preparation.Google Scholar
  51. 51.
    S. Arnott, R. Chandrasekaran, I.H. Hall and L.C. Puigjaner, Heteronomous DNA, Nucleic Acids Res., 11, 4141 (1983).PubMedCrossRefGoogle Scholar
  52. 52.
    S.N. Rao and P.A. Kollman, On the role of uniform and mixed sugar puckers in DNA double-helical structures, J. Amer. Chem. Soc, 107, 1611 (1985).CrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1986

Authors and Affiliations

  • V. I. Poltev
    • 1
  • A. V. Teplukhin
    • 2
  • V. P. Chuprina
    • 2
  1. 1.Institute of Biological PhysicsUSSR Academy of SciencesPushchino, Moscow RegionRussia
  2. 2.Research Computing CenterUSSR Academy of SciencesPushchino, Moscow RegionRussia

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