Bending of DNA

If one traces a longer stretch of a DNA molecule in solution, a clear divergence from linearity becomes evident. Tliermally induced structural fluctuations allow a bending of DNA, which is why long DNA molecules are described as a random cod. This bending of the DNA occurs in molecules with a length of more than approx. 200 bp. 

The bending of shorter DNA fragments can be attained via specific sequence with intrinsic bending abUity as well as by binding of proteins. 

Tlie divergence of the DNA conformation from a rod-like structine is observed to a variable extent. The DNA can be slightly curved or abruptly kinked. 

If the DNA is only slightly bent, as observed for the nucleosome-boimd DNA, then the required deformation energy is distributed over many base pairs. Tlie energy requirement per base pair is small and can easily be provided by the interaction energy with the protein. Furthermore, such bending displays little sequence specificty. 

Kinking of the DNA is observed, for example, in the DNA complex of the CAP protein, as well as for the TATA-box binding protein. In the complex of the CAP protein there are two successive kinks in the DNA, each of which lead to a bending of ca. 40°, resulting in a net bend of 80°-90° (Fig. 1.15). 

---

The sharp bend of DNA at the TATA box induced by TBP binding is favorable for the formation of the complete DNA control module in particular, for the interaction of specific transcription factors with TFIID. Since these factors may bind to DNA several hundred base pairs away from the TATA box, and at the same time may interact with TBP through one or several TAFs, there must be several protein-DNA interactions within this module that distort the regular B-DNA structure (see Figure 9.2). The DNA bend caused by the binding of TBP to the TATA box is one important step to bring activators near to the site of action of RNA polymerase. 

Ikeda K, Nagano K, Kawakami K (1993) Possible imphcations of Spl-induced bending of DNA on synergistic activation of transcription. Gene 136(l-2) 341-343 Ishida T, Hamano A, Koiwa T, Watanabe T (2006) 5 long terminal repeat (LTR)-selective methy-lation of latently infected HIV-1 provirus that is demethylated by reactivation signals. Retrovirology 3 69... 

Fig. 1.13. Bending of DNA as a result of charge neutralization by a DNA-binding protein. The negatively charged DNA bends upon binding the positively charged protein surface. On the side of the DNA facing away from the protein excess negative charges build up and repel each other. After Strauss Maher (1994).

Fig. 1.14. Intrinsic bending of DNA via periodic repeat of (dA)5 6 sequences. An intrinsic bending of DNA of ca. 18° is induced per (dA)s 6 sequence. Poly-dA repeats in 10 bp steps (the rise of the DNA) result in a strong bending of the DNA, since in this configuration the axis of bending lies on the same side of the DNA.

Fig. 1.16. Bending of DNA in the TATA box. The DNA is kinked in the complex of the TATA box binding protein (yeast) with the 8 base pair TATA box (Kim et al., 1993). The DNA is deformed in the region near the kink the minor groove, which faces the protein, is clearly widened. Molscript drawing (Kraulis, 1991).

What Purpose does the Bending of DNA Serve for Regulatory Processes ... 

Fig. 1.17. The significance of the bending of DNA for protein-protein interactions. DNA-bound proteins, which would not interact if associated with linear DNA, can be brought together through intrinsic or protein-induced bending of the intervening sequences. The bending of the DNA creates a high local concentration of the two proteins and thus enables their effective interaction.

T.K. Chiu and R E. Dickerson. 2000. 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium J. Mol. Biol. 301 915-945. (PubMed)... 

The bending of DNA has been studied by joining a pair of triplex forming oligonucleotides by a variable length linker. ... 

---