Electrostatic potential mapping of nucleic acid constituents: I. Guanine, cytosine and the G-C base pair

  • Antl Kumar
  • P C Mishra
Physical and Theoretical


Electrostatic potential maps of guanine, cytosine and the G-C base pair in the Watson-Crick and Hoogsteen configurations have been studied using a mapping dipole of length 1Åand strength 1 Debye. Net charges on the atoms of the molecules were obtained by the MNDO molecular orbital method. Several closest distances of approach (CDA) between the mapping dipole and atomic sites of the molecules were considered and potentials calculated using interactions of net charges keeping the dipole in the molecular plane in each case. While on one hand this work supports the existence of potential minima obtained by monopole isopotential mapping, on the other it yields additional useful information, e.g. electric field directions which correspond to the directions of probable hydrogen bonds with other species. A deep localized potential region is observed around N4 of cytosine in the Hoogsteen configuration while it is not present in the Watson-Crick base pairing.


Cytosine Guanine Molecular Plane Minimum Potential Energy Electric Field Direction 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Aoki A 1976aJ. Chem. Soc, Chem. Commun. 748Google Scholar
  2. Aoki A 1976bActa Cryst. B32 1454CrossRefGoogle Scholar
  3. Arnott S, Dover S D and Wonacott A J 1969Acta Cryst. B25 2192CrossRefGoogle Scholar
  4. Bonaccorsi R, Pullman A, Scrocco E and Tomasi J 1972Theor. Chim. Acta 24 51CrossRefGoogle Scholar
  5. Brooks P and Lawley P D 1962J. Chem. Soc. 1348Google Scholar
  6. Budowsky E I 1976Prog. Nucleic Acid Res. Mol. Biol. 16 125CrossRefGoogle Scholar
  7. Dehand J and Jordanov J 1976J. Chem. Soc, Chem. Commun. 598Google Scholar
  8. Dewar M J S and Thiel W 1977J. Am. Chem. Soc. 99 4899CrossRefGoogle Scholar
  9. Fiskin A M and Beer M 1965Biochem. J. 1289Google Scholar
  10. Gellert R W and Bau R 1975J. Am. Chem. Soc. 97 7379CrossRefGoogle Scholar
  11. Goodgame D M L, Jeeves I, Phillips F L and Skapski A C 1975Biochim. Biophys. Acta 378 153Google Scholar
  12. Hoogsteen K 1963Acta Cryst. 16 907CrossRefGoogle Scholar
  13. Jardetzky O, Pappas P and Wade N G 1963J. Am. Chem. Soc. 85 1657CrossRefGoogle Scholar
  14. Kriek E 1980 inCarcinogenesis: Fundamental mechanism and environmental effects (eds) B Pullman, POP Ts’o and H Gelboin (Boston: D Reidel) p. 103Google Scholar
  15. Lavery R and Pullman B 1982Nucleic Acid Res. 10 4383CrossRefGoogle Scholar
  16. Lawley P D 1957Proc. Chem. Soc. (London) 290Google Scholar
  17. Lawley P D 1961Prog. Nucleic Acid Res. Mol. Biol. 5 89CrossRefGoogle Scholar
  18. Lawley P D and Thatcher G J 1970Biochem. J. 116 643Google Scholar
  19. Loveless A 1969Nature (London) 223 206CrossRefGoogle Scholar
  20. Millard M M, Macquet J P and Theophanides T 1975Biochem. Biophys. Acta 402 166Google Scholar
  21. Mishra P C and Tewari R D 1987Int. J. Quantum Chem. 32 181CrossRefGoogle Scholar
  22. Pal B C 1962Biochemistry 1 558CrossRefGoogle Scholar
  23. Politzer P, Laurence P R and Jayasuriya K 1985Environ. Health Perspec. 61 191CrossRefGoogle Scholar
  24. Price S L, Stone A J and Alderton M 1984Mol. Phys. 52 987CrossRefGoogle Scholar
  25. Pullman A and Pullman B 1981Q. Rev. Biophys. 14 289CrossRefGoogle Scholar
  26. Scrocco E and Tomasi J 1978Adv. Quantum Chem. 11 115CrossRefGoogle Scholar
  27. Sokalski W A 1987J. Mol. Struct. (Theochem.) 150 235CrossRefGoogle Scholar
  28. Sletten E and Lie B 1976Acta Cryst. B32 3301CrossRefGoogle Scholar
  29. Szalda D J, Marzilli L G and Kistenmacher T J 1975Biochem. Biophys. Res. Commun. 63 601CrossRefGoogle Scholar
  30. Voet D and Rich A 1970Prog. Nucleic Acid Res. Mol. Biol. 10 183CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 1989

Authors and Affiliations

  • Antl Kumar
    • 1
  • P C Mishra
    • 1
  1. 1.Department of PhysicsBanaras Hindu UniversityVaranasiIndia

Personalised recommendations