Protein–DNA Complexes: Specific


Sequence‐specific DNA‐binding proteins recognize and interact with discrete base sequences in the genome to regulate fundamental metabolic processes.

Keywords: DNA‐binding proteins; DNA sequence recognition; DNA structure

Figure 1.

Points of recognition in the major (M) and minor (m) grooves of DNA for each of the four base pairs. a, electron acceptor; d, electron donor; me, methyl group. Hydrogen bonding in base pairs is indicated by dashed lines. dR in circles denotes the deoxyribose‐phosphate backbone of DNA.

Figure 2.

Examples of amino acid–base pair interactions. (a) Arginine bonding to guanine. (b) Serine bonding to adenine. (c) Asparagine bonding to adenine. (d) Cysteine double contact to adenine and guanine of adjacent base pairs. In (d), the adenine is attached to the opposite strand relative to the guanine but the bases have been drawn on the same plane. Hydrogen bonds are denoted by dashed lines.



Choo Y and Klug A (1997) Physical basis of a protein–DNA recognition code. Current Opinion in Structural Biology 7: 117–125.

Chytil M and Verdine GL (1996) The Rel family of eucaryotic transcription factors. Current Opinion in Structural Biology 6: 91–100.

Harrington RE (1992) DNA curving and bending in protein–DNA recognition. Molecular Microbiology 6: 2549–2555.

Hegde RS, Wang A‐F, Kim SS and Schapira M (1998) Subunit rearrangement accompanies sequence‐specific DNA binding by the bovine papillomavirus‐1 E2 protein. Journal of Molecular Biology 276: 797–808.

Kielkopf CL, White S, Szewczyk JW et al. (1998) A structural basis for recognition of A·T and T·A base pairs in the minor groove of B‐DNA. Science 282: 111–115.

Kim E, Albrechtsen N and Deppert W (1997) DNA‐conformation is an important determinant of sequence‐specific DNA binding by tumor suppressor p53. Oncogene 15: 857–869.

Kim Y, Geiger JH, Hahn S and Sigler PB (1993) Crystal structure of a yeast TBP/TATA‐box complex. Nature 365: 512–519.

Koudelka GB (1998) Recognition of DNA structure by 434 repressor. Nucleic Acids Research 26: 669–675.

Lesser DR, Kurpiewski MR, Waters T, Connolly BA and Jen‐Jacobson L (1993) Facilitated distortion of the DNA site enhances EcoRI endonuclease‐DNA recognition. Proceedings of the National Academy of Sciences of the USA 90: 7548–7552.

Schwabe JWR (1997) The role of water in protein–DNA interactions. Current Opinion in Structural Biology 7: 126–134.

Vashee S, Melcher K, Deng WV, Johnston SA and Kodadek T (1998) Evidence for two modes of cooperative DNA binding in vivo that do not involve protein–protein interactions. Current Biology 8: 452–458.

Wong JM and Bateman E (1994) TBP–DNA interactions in the minor groove discriminate between A:T and T:A base pairs. Nucleic Acids Research 22: 1890–1896.

Further Reading

Berg OG and von Hippel PH (1988) Selection of DNA binding sites by regulatory proteins. Trends in Biochemical Sciences 13: 207–211.

Gehring WJ, Affolter M and Burglin T (1994) Homeodomain proteins. Annual Review of Biochemistry 63: 487–526.

Harrison SC and Aggarwal AK (1990) DNA‐recognition by proteins with the helix–turn–helix motif. Annual Review of Biochemistry 59: 933–969.

Lilley DM (ed.) (1995) DNA–Protein Structural Interactions. Oxford: IRL Press.

Pabo CO and Sauer RT (1992) Transcription factors: structural families and principals of DNA recognition. Annual Review of Biochemistry 61: 1053–1095.

Raumann BE, Brown BM and Sauer RT (1994) Major groove DNA recognition by β‐sheets: the ribbon–helix–helix family of gene regulatory proteins. Current Biology 4: 36–43.

Travers A (1993) DNA–Protein Interactions. London: Chapman and Hall.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Strauch, Mark A(Apr 2001) Protein–DNA Complexes: Specific. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0001357]