A-DNA bending

There is experimental evidence that DNA bending per se is functionally important in transcription [133-141], for example, by bringing two nonadjacent regions of the double helix close together. The presence of pre-bent A-tracts does influence protein-DNA interactions [142, 143]. Most interestingly, the functional replacement of a DNA-bending protein binding site by a pre-bent DNA site (e.g., A-tracts) has been demonstrated experimentally in several cases [144-148]. 

Lac repressor binds to both the major and the minor grooves inducing a sharp bend in the DNA... 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

Steitz has suggested that DNA bending by CAP could contribute to activation of transcription by looping the DNA around CAP to provide for contacts between RNA polymerase and DNA upstream of the CAP-binding site. Such a model could explain how CAP can activate transcription from a variety of distances from the RNA polymerase-binding site since the size of the loop could vary. 

Some of the procaryotic DNA-binding proteins are activated by the binding of an allosteric effector molecule. This event changes the conformation of the dimeric protein, causing the helix-tum-helix motifs to move so that they are 34 A apart and able to bind to the major groove. The dimeric repressor for purine biosynthesis, PurR, induces a sharp bend in DNA upon binding caused by insertion of a helices in the minor groove between the two... 

The HMG (high mobility group) box is a DNA-binding domain found in several transcription factors, that can in some cases bend DNA. Some members of this protein family recognize a unique DNA sequence, whereas others bind to a common DNA conformation. 

The interstrand cross-link also induces DNA bending.72 X-ray and NMR studies on this adduct show that platinum is located in the minor groove and the cytosines of the d(GC) base pair involved in interstrand cross-link formation are flipped out of the helix stack and a localized Z-form DNA is observed.83-85 This is a highly unusual structure and very distorting—implications for differential repair of the two adducts have been addressed. Alternatively, the interstrand cross-link of the antitumor inactive trans-DDP is formed between a guanine (G) and its complementary cytosine (C) on the same base p a i r.86,87/ nms- D D P is sterically incapable of producing 1,2-intrastrand adducts and this feature has been cited as a dominant structural reason for its lack of antitumor efficacy. It is clear that the structural distortions induced on the DNA are very different and likely to induce distinctly different biological consequences. 

Lia G, Praly E, Ferreira H, Stockdale C, Tse-Dinh YC, Dunlap D, Croquette V, Bensimon D, Owen-Hughes T (2006) Direct observation of DNA distortion by the RSC complex. Mol Cell 21 417 25 Lorch Y, Davis B, Kornberg RD (2005) Chromatin remodeling by DNA bending, not twisting. Proc Natl Acad Sci U S A 102 1329-1332 Luger K (2006) Dynamic nucleosomes. Chromosome Res 14 5-16... 

Nucleolin together with HnRNP D has been shown to form the LRl transcription factor. LRl is a B cell-specific, sequence-specific DNA binding activity that regulates transcription in activated B cells (Hanakahi et at, 1997 Hanakahi and Maizels, 2000). DNA bending induced by nucleolin and hnRNP D might regulate the transcriptional activation by LRl (Hanakahi and Maizels, 2000). 

B. Audit, C. Vaillant, A. Arneodo, Y. d Aubenton-Carafa, and C. Thermes, Long-range correlations between DNA bending sites Relation to the structure and dynamics of nucleo-somes. J. Mol. Biol. 316, 903-918 (2002). 

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