DNA-protein interactions in the regulation of gene expression

Part of the Topics in Molecular and Structural Biology book series (TMSB)


In this paper we describe a number of approaches to the nature and specificity of DNA-protein interactions involved in the regulation of gene expression at the transcriptional level. We discuss primarily the binding of ‘single-specific-site’ regulatory proteins to DNA targets. This involves consideration of several aspects of the specificity of DNA-protein interactions, including: (1) the combinatorial specification of the number of base pairs required to define a unique binding site in a genome of given size; (2) the structure of DNA and protein binding sites, including structural complementarity and steric aspects; (3) the energetics of the binding interaction, including both specific and non-specific binding; (4) the thermodynamics and kinetics of the overall interaction, as determined by the net binding free energy of specific complex formation and the effects of competing sites; and (5) equilibrium binding selection, which determines the actual level of saturation of the specific (regulatory) target under various environmental conditions. These aspects are all interdependent, and a coherent picture of the specificity of such interactions can be obtained only by considering them all in context. Such an approach has been set forth by us previously, in part, in von Hippel and Berg (1986), and portions of this overview are taken directly from that treatment. In conclusion, we consider how these ideas modulate the evolutionary ‘design’ of regulatory proteins, as well as the formulation of purification procedures and binding assays for these proteins, and how these approaches may apply in vivo.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Anderson, J. E., Ptashne, M. and Harrison, S. C. (1987). Structure of the repressor-operator complex of bacteriophage 434. Nature, 326, 846–852CrossRefGoogle Scholar
  2. Berg, O. G. and von Hippel, P. H. (1987). Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and applications to operators and promoters. J.Mol. Biol., 193, 723–750CrossRefGoogle Scholar
  3. Berg, O. G. and von Hippel, P. H. (1988). Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein (CRP) to recognition sites. J. Mol. Biol., in pressGoogle Scholar
  4. Berg, O. G., Winter, R. B. and von Hippel, P. H. (1982). How do genome-regulatory proteins locate their DNA target sites? Trends Biochem. Sci., 7, 52–55CrossRefGoogle Scholar
  5. deHaseth, P. L., Lohman, T. M. and Record, M. T., Jr (1977). Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release. Biochemistry, 16, 4783–4790CrossRefGoogle Scholar
  6. deHaseth, P. L. Lohman, T. M., Record, M. T., Jr and Burgess, R. R. (1978). Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: differences in the binding behavior of core and holoenzyme. Biochemistry, 17, 1612–1622CrossRefGoogle Scholar
  7. Dickson, R. C., Abelson, J. N., Barnes, W. M. and Reznikoff, W. S. (1975). Genetic regulation. lac control region. Science, 182, 27–35CrossRefGoogle Scholar
  8. Fairfield, F. R., Newport, J. W., Dolejsi, M. K. and von Hippel, P. H. (1983). On the processivity of DNA replication. J. Biomol. Struct. Dyn., 1, 715–727CrossRefGoogle Scholar
  9. Goeddel, D. V., Yansura, D. G. and Caruthers, M. H. (1978). How lac repressor recognizes lac operator. Proc. Natl Acad. Sci. USA, 75, 3578–3582CrossRefGoogle Scholar
  10. Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. and Dickerson, R. E. (1985). The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc. Natl Acad. Sci. USA, 82, 1376–1380CrossRefGoogle Scholar
  11. Kowalczykowski, S. C., Lonberg, N., Newport, J. W. and von Hippel, P. H. (1981). Interactions of T4 coded gene 32-protein with nucleic acids. I. Characterization of the binding interactions. J. Mol. Biol., 145, 75–104CrossRefGoogle Scholar
  12. Liu-Johnson, H.-N., Gartenberg, M. R. and Crothers, D. M. (1986). The DNA binding domain and bend angle of E. coli CAP protein. Cell, 47, 995–1005CrossRefGoogle Scholar
  13. Melchior, W. B., Jr and von Hippel, P. H. (1973). Alteration of the relative stability of dA · dT and dG · dC base pairs in DNA. Proc. Natl Acad. Sci. USA, 70, 298–302CrossRefGoogle Scholar
  14. Mossing, M. C. and Record, M. T., Jr (1985). Thermodynamic origins of specificity in the lac repressor-operator interactions. Adaptability in the recognition of mutant operator sites. J. Mol. Biol., 186, 295–305CrossRefGoogle Scholar
  15. O’Gorman, R. B., Rosenberg, J. M., Kallai, O. B., Dickerson, R. E., Itakura, K., Riggs, A. D. and Matthews, K. S. (1980). Equilibrium binding of inducer to lac repressor-operator DNA complex. J. Biol. Chem., 255, 10107–10114Google Scholar
  16. Ohlendorf, D. H., Anderson, W. F., Fisher, R. G., Takeda, Y. and Matthews, B. W. (1982). The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature, 298, 718–723CrossRefGoogle Scholar
  17. Ptashne, M., Jeffrey, A., Johnson, A. D., Maurer, R., Meyer, B. J., Pabo, C. O., Roberts, T. M. and Sauer, R. T. (1980). How the λ repressor and cro work. Cell, 19, 1–11CrossRefGoogle Scholar
  18. Record, M. T., Jr, deHaseth, P. L. and Lohman, T. M. (1977). Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. Biochemistry, 16, 4791–4796CrossRefGoogle Scholar
  19. Record, M. T., Jr, Lohman, T. M. and deHaseth, P. L. (1976). Ion effects on ligand-nucleic acid interactions. J. Mol. Biol., 107, 145–158CrossRefGoogle Scholar
  20. Revzin, A. and von Hippel, P. H. (1977). Direct measurement of association constants for the binding of Escherichia coli lac repressor to non-operator DNA. Biochemistry, 16, 4769–4776CrossRefGoogle Scholar
  21. Schneider, T. D., Stormo, G. D., Gold, L. and Ehrenfeucht, A. (1986). Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415–431CrossRefGoogle Scholar
  22. Seeman, N. C. Rosenberg, J. M. and Rich, A. (1976). Sequence-specific recognition of double-helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA, 73, 804–808CrossRefGoogle Scholar
  23. Tronrud, D. E., Holden, H. M. and Matthews, B. W. (1987). Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond. Science, 235, 571–574CrossRefGoogle Scholar
  24. von Hippel, P. H. (1979). On the molecular bases of the specificity of interaction and transcriptional proteins with genome DNA. In Goldberger, R. F. (ed.), Biological Regulation and Development, Plenum, New York, 279–347CrossRefGoogle Scholar
  25. von Hippel, P. H., Bear, D. G., Winter, R. B. and Berg, O. G. (1982). Molecular aspects of promoter function: An overview. In Chamberlain, M. and Rodriquez, R. (eds), Promoters: Structure and Function, Praeger, New York, 3–33Google Scholar
  26. von Hippel, P. H. and Berg, O. G. (1986). On the specificity of DNA-protein interactions. Proc. Natl Acad. Sci.USA, 83, 1608–1612CrossRefGoogle Scholar
  27. von Hippel, P. H. and Berg, O. G. (1989). Facilitated target location in biological systems. J. Biol. Chem., 264, 675–678 (minireview)Google Scholar
  28. von Hippel, P. H. and Fairfield, F. R. (1985). Thermodynamic aspects of the regulation of protein synthesis in bacteria. Pure Appl. Chem., 57, 45–56Google Scholar
  29. von Hippel, P. H. and McGhee, J. D. (1972). DNA-protein interactions. Ann. Rev. Biochem., 41, 231–300CrossRefGoogle Scholar
  30. von Hippel, P. H., Revzin, A., Gross, C. A. and Wang, A. C. (1974). Non-specific DNA binding of genome regulating proteins as a biological control mechanism. I. The lac Operon: Equilibrium aspects. Proc. Natl Acad. Sci. USA, 71, 4808–4812Google Scholar
  31. Weintraub, H. and Groudine, M. (1976). Chromosomal subunits in active genes have an altered conformation. Science, 193, 848–856CrossRefGoogle Scholar
  32. Winter, R. B., Berg, O. G. and von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. III. The E. coli lac repressor-operator interaction: Kinetic measurements and conclusions. Biochemistry, 20, 6961–6977CrossRefGoogle Scholar
  33. Winter, R. B. and von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. II. The E. coli lac repressor-operator interaction: equilibrium measurements. Biochemistry, 20, 6948–6960CrossRefGoogle Scholar
  34. Woodbury, C. P., Jr, Hagenbuchle, O. and von Hippel, P. H. (1980). DNA site recognition and reduced specificity of the EcoRI endonuclease. J. Biol. Chem., 255, 11534–11546Google Scholar
  35. Woodbury, C. P., Jr and von Hippel, P. H. (1981). Relaxed sequence specificities of EcoRI endonuclease and methylase: Mechanisms, possible practical applications and uses in defining protein-nucleic acid recognition mechanisms. In Chirikjian, J. (ed.), The Restriction Enzymes, Elsevier, Amsterdam, 181–207Google Scholar
  36. Yarus, M. (1969). Recognition of nucleotide sequences. Ann. Rev. Biochem., 38, 841–880CrossRefGoogle Scholar

Copyright information

© The Contributors 1989

Authors and Affiliations

There are no affiliations available

Personalised recommendations