1. The DNA structures in approximately 40 available crystals of DNA-protein complexes were analyzed in terms of the local sequence-specific bending, and in terms of the overall structure. (i) Local DNA anisotropy. DNA folding occurs predominantly by means of the mini-kinks, directed toward the major groove and localized in the pyrimidine-purine YR dimers (CA,TG, TA, CG) and in AG:CT steps. Bending toward the major groove is accompanied by DNA unwinding, the tendency consistent with the rules of DNA """"""""conformational mechanics"""""""" established by us earlier for """"""""pure"""""""" unbound B-DNA. (ii) Overall tertiary folds. DNA is often bent into non-planar loops, resembling the path of the double helix in the nucleosome. This non-planarity correlates with the non-random periodic distribution of the YR and AG dimers in the binding sites. This feature is expected to facilitate the binding of regulatory proteins to negatively supercoiled DNA in vivo. 2. DNA Bending in the Complex with p53 .Based on the X-ray data, a detailed model was proposed for the core domain of the tumor suppressor protein p53 bound to the functionally important response element Waf1. Four subunits of p53 are bound to the 20 bp long response element in a regular staggered array with dyad symmetry. DNA is bent by 25-30 degrees in the highly conserved C(A/T)(T/A)G parts of the Waf1 site. Importantly, this bending, caused by the protein-protein stereochemical clashes, is consistent with the DNA sequence-dependent anisotropy described above. This detailed model opens the possibilities for analyzing the human genome database aimed at establishing general mechanisms of p53 tumor suppressor binding to DNA organized in chromatin.
