Journal of Biosciences

, Volume 8, Issue 3–4, pp 645–656 | Cite as

Recognition schemes for protein-nucleic acid interactions

  • Girjesh Govil
  • N. Y. Kumar
  • M. Ravi Kumar
  • R. V. Hosur
  • Kunal B. Roy
  • H. Todd Miles


The molecular forces involved in protein-nucleic acid interaction are electrostatic, stacking and hydrogen-bonding. These interactions have a certain amount of specificity due to the directional nature of such interactions and the spatial contributions of the steric effects of different substituent groups. Quantum chemical calculations on these interactions have been reported which clearly bring out such features.

While the binding energies for electrostatic interactions are an order of magnitude higher, the differences in interaction energies for structures stabilised by hydrogen-bonding and stacking are relatively small. Thus, the molecular interactions alone cannot explain the highly specific nature of binding observed in certain segments of proteins and nucleic acids. It is therefore logical to assume that the sequence dependent three dimensional structures of these molecules help to place the functional groups in the correct geometry for a favourable interaction between the two molecules.

We have carried out 2D-FT nuclear magnetic resonance studies on the oligonucleotide d-GGATCCGGATCC. This oligonucleotide sequence has two binding sites for the restriction enzyme Bam H1. Our studies indicate that the conformation of this DNA fragment is predominantly B-type except near the binding sites where the ribose ring prefers a3E conformation. This interesting finding raises the general question about the presence of specificity in the inherent backbone structures of proteins and nucleic acids as opposed to specific intermolecular interactions which may induce conformational changes to facilitate such binding.


Protein-nucleic acid interactions nuclear magnetic resonance quantum chemistry calculation 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Arnott, S. (1971)Prog. Biophys. Mol. Biol.,21, 265.CrossRefGoogle Scholar
  2. Arnott, S. and Hukins, P. W. L. (1972)Biochem. J.,130, 453.PubMedGoogle Scholar
  3. Aue, P., Bartholdi, E. and Ernst, R. R. (1976)J. Chem. Phys.,64, 2229.CrossRefGoogle Scholar
  4. Brown (1970)Biochim. Biophys, Acta.,213, 282.Google Scholar
  5. Bruskov, V. I. (1975)Molek. Biol.,9, 304.Google Scholar
  6. Caillet, J. and Claverie, P. (1975)Acta. Crystalogr.,31A, 448.CrossRefGoogle Scholar
  7. Claverie, P. (1978) inIntermodular Interactions; From Diatomics to Biopolymers, (ed. B. Pullman) (New York: Wiley) p. 69.Google Scholar
  8. Gabbay, E. J., Dastefano, R. and Sanford, K. (1972)Biochem. Biophys. Res. Commun.,46, 155.PubMedCrossRefGoogle Scholar
  9. Govil, G. and Hosur, R. V. (1982)Conformation of Biological Molecules, (New York: Springer Verlag).Google Scholar
  10. Hosur, R. V. (1980)Curr. Sci.,49, 928.Google Scholar
  11. Hosur, R. V., Kumar, N. V. and Govil, G. (1981)Int. J. Q. Chem.,20, 23.CrossRefGoogle Scholar
  12. Hosur, R. V. and Pohorille, A., (1981)Int. J. Q. Chem.,20, 33.CrossRefGoogle Scholar
  13. Hosur, R. V., Ravi Kumar, M., Roy, K. B., Tan, Zu-Kun, Miles, H. T. and Govil, G. (1985) inMagnetic Resonance in Biology and Medicine (eds G. Govil, C. L. Khetrapal and A. Saran) (New Delhi: Tata McGraw-Hill).Google Scholar
  14. Helene, C. (1977)FEBS Lett.,74, 10.PubMedCrossRefGoogle Scholar
  15. Helene, C. and Lancelot, G. (1982)Prog. Biophys. Mol. Biol.,39, 168.Google Scholar
  16. Kumar, A., Wagner, G., Ernst, R. R. and Wuthrich, K. (1980)Biochem. Biophys. Res. Commun.,96, 1156.PubMedGoogle Scholar
  17. Kumar, N. V. and Govil, G. (1982) inConformation in Biology, (eds R. Srinivasan and R. H. Sarma) (New York: Adenine Press) p. 313.Google Scholar
  18. Kumar, N. V. and Govil, G. (1984a)Biopolymers,23, 1979.PubMedCrossRefGoogle Scholar
  19. Kumar, N. V. and Govil, G. (1984b)Biopolymer,23, 1995.CrossRefGoogle Scholar
  20. Kumar, N. V. and Govil, G. (1984c)Biopolymer 23, 2009.CrossRefGoogle Scholar
  21. Le Fevre, R. J. W. (1965)Adv. Phys. Org. Chem.,3, 1.CrossRefGoogle Scholar
  22. Pople, J. A. and Beveridge, D. L. (1970)Approximate Molecular Orbital Theory (New York: McGraw-Hill).Google Scholar
  23. Scheek, R. M., Zuiderweg, E. R. P., Boelens, R., Van Gunsteress, W. F. and Kaptein, R. (1985) inMagnetic Resonance in Biology and Medicine (eds G. Govil, C. L. Khetrapal and A. Saran), (New Delhi: Tata McGrawHill).Google Scholar
  24. Seemann, N. C., Rosenberg, J. M. and Rich, A. (1976)Proc. Natl. Acad. Sci. USA,73, 804.CrossRefGoogle Scholar

Copyright information

© Printed in India 1985

Authors and Affiliations

  • Girjesh Govil
    • 1
  • N. Y. Kumar
    • 1
  • M. Ravi Kumar
    • 1
  • R. V. Hosur
    • 1
  • Kunal B. Roy
    • 2
  • H. Todd Miles
    • 3
  1. 1.Tata Institute of Fundamental ResearchBombayIndia
  2. 2.All India Institute of Medical SciencesNew DelhiIndia
  3. 3.National Institutes of HealthBethesdaUSA

Personalised recommendations