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CAP Binding Sites Reveal Pyrimidine-Purine Pattern Characteristic of DNA Bending

1990; Taylor & Francis; Volume: 8; Issue: 2 Linguagem: Inglês

10.1080/07391102.1990.10507803

1538-0254

Ann Barber, Victor B. Zhurkin,

RNA Interference and Gene Delivery

Abstract To investigate the intrinsic bending of DNA at sites where proteins bind, we analyzed catabolite gene activator protein (CAP) binding sites and various operators from the viewpoint of DNA bending flexibility. Theoretical conformational analysis, DNase I digestion and x-ray crystallography data indicate that bending of B-DNA is highly anisotropic and sequence-dependent. Certain dimers prefer to bend into the major groove (“major-philic”) and others prefer to bend into the minor groove (“minor-philic” dimers). From these data we considered TA CG, CA:TG and GG:CC as major-philic dimers and AT, AA:TT and GT:AC as minor-philic ones. Analysis of 31 CAP binding sites has identified strong major-philic tendencies 5–7 base pairs (bp) away from the center. In addition, we found minor-philic poly-A tracts extending 4–5 bp away from the proposed major-philic bends. Finally, to analyze the central regions we followed the lead of Shumilov and classified the DNA sites by their spacer lengths [V.Y. Shumilov, Mol. Biol. (Mosk) 21, 168–187 (1987)]. In this way, we identified two subsets of CAP binding sites: one with 6 bp between the TGTGA:TCACA consensus boxes (N6-set) and one with 8 central bp (N8-set). We discovered that the dimer at the center of an N6-set site was usually major-philic, whereas at the center of an N8-set site more often minor-philic. Analysis of phages 434, P22, λ and trp operators revealed similar results. In conclusion, our data show that CAP binding sites have major-philic and minor-philic dimers at specific positions; the location of these dimers may facilitate wrapping of DNA around CAP. A similar pattern is seen in nucleosomes.