DNA Structure Changes Coupled to Protein Binding


Protein‐induced DNA distortions facilitate the interactions between proteins bound to non‐adjacent sites on DNA. Correct assembly of these macromolecular complexes is necessary for DNA transcription, recombination, repair and replication.

Keywords: DNA bending; DNA kinking; sequence‐dependent DNA structure; protein–DNA interactions; transcriptional regulation

Figure 1.

DNA constructs used for the phasing analysis. Intrinsic DNA bend (on the left in each part of the figure) is separated by a variable spacer (shown in yellow) from the protein‐induced bend (on the right). In (a) and (f), the two bends are of opposite direction and cancel each other. Bending is additive in (c) and (d), which results in slowest gel mobility.

Figure 2.

Homodimer of catabolite activator protein (CAP) bends DNA by 90°, mostly through two kinks separated by a helical turn. In this case, DNA kinking is achieved without side‐chain intercalation. DNA trajectory is shown as a white line tracing the centres of DNA base pairs. The structure was solved in the laboratory of T. Steitz.

Figure 3.

A complex between TATA box‐binding protein (TBP) (red), transcription factor related to RNA polymerase II B (TFIIB) (blue) and transcription factor related to RNA polymerase II A (TFIIA) (green) is assembled in the initiation step of transcription. This quaternary complex has been created by combining ternary structures of TBP/TFIIB/DNA and TBP/TFIIA/DNA. A piece of ideal B‐DNA is added at both sides of the original DNA structure. TBP bends DNA away from its surface by intercalating two side‐chains at sites separated by 6 base pairs. The structures were solved in the laboratories of S. Burley and P. Sigler.

Figure 4.

DNA wraps around the nucleosomal core that includes pairs of H2A, H2B, H3 and H4 histones. The structure was solved in the laboratory of T. Richmond.

Figure 5.

A quartenary complex of Fos (red), Jun (blue) and nuclear factor of activated T cells (NFAT) (green) bound to DNA from the distal antigen‐receptor response element. DNA bending enables additional contacts between proteins. The structure was solved in the laboratory of S. Harrison.

Figure 6.

Ternary complex of MATa1 (red), MATα2 (blue) and DNA, which is smoothly bent towards the proteins. The structure was solved in the laboratory of C. Wolberger.

Figure 7.

Lymphoid enhancer factor 1 (red) is an architectural protein that bends DNA away from its surface by side‐chain intercalation. The structure was solved in the laboratories of R. Grosschedl and P. Wright.



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Further Reading

Bustamante C and Rivetti C (1996) Visualizing protein–nucleic acid interactions on a large scale with the scanning force microscope. Annual Review of Biophysics and Biomolecular Structure 25: 395–429.

Drew HR and Travers AA (1985) DNA bending and its relation to nucleosome positioning. Journal of Molecular Biology 186: 773–790.

Giese K, Kingsley C, Kirschner JR and Grosschedl R (1995) Assembly and function of a TCRα enhancer complex is dependent on LEF‐1‐induced DNA bending and multiple protein–protein interactions. Genes and Development 9: 995–1008.

Harrington RE (1993) Studies of DNA bending and flexibility using gel electrophoresis. Electrophoresis 14: 732–746.

Juo ZS, Chiu TK, Leiberman PM et al. (1996) How proteins recognize the TATA box. Journal of Molecular Biology 261: 239–254.

Leonard DA, Rajaram N and Kerppola TK (1997) Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun. Proceedings of the National Academy of Sciences of the USA 94: 4913–4918.

Olson WK and Zhurkin VB (1996) Twenty years of DNA bending. In: Sarma RH and Sarma MH (eds) Biological Structure and Dynamics, vol. II, pp. 341–370. Schenectady, NY: Adenine Press.

Perez‐Martin J and de Lorenzo V (1997) Clues and consequences of DNA bending in transcription. Annual Review of Microbiology 51: 593–628.

Werner MH and Burley SK (1997) Architectural transcription factors: proteins that remodel DNA. Cell 88: 733–736.

Wu HM and Crothers DM (1984) The locus of sequence‐directed and protein‐induced DNA bending. Nature 308: 509–513.

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Dlakic, Mensur, and Kerppola, Tom K(Apr 2001) DNA Structure Changes Coupled to Protein Binding. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0003009]