title: CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending.
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 lambda 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.
authors.affiliation: Laboratory of Mathematical Biology NCI, National Institutes of Health, Bethesda, MD 20892.
authors.forename: A M
authors.initials: AM
authors.lastname: Barber
authors.forename: V B
authors.initials: VB
authors.lastname: Zhurkin
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D002373:Cyclic AMP Receptor Protein / Q000235:genetics*; D004247:DNA / Q000737:chemistry*; D003850:Deoxyribonuclease I; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D011685:Purine Nucleotides / Q000235:genetics*; D011742:Pyrimidine Nucleotides / Q000235:genetics*; D013237:Stereoisomerism; D014961:X-Ray Diffraction
chemical_list: D002373:Cyclic AMP Receptor Protein; D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D004247:DNA; D003850:Deoxyribonuclease I