title: Kinematic model for B-DNA.
abstract: X-ray structure analysis of B-DNA double helix with sequence C-G-C-G-A-A-T-T-C-G-C-G has revealed several sequence-dependent structural features. Four of these are shown in this paper to be related to one another by simple structural or kinematic principles: (i) the correlation between glycosyl torsion and chi and main chain C4'--C3' torsion angle delta, (ii) the observations that purines prefer larger phi and delta angles than do pyrimidines, (iii) the anticorrelation of phi or of delta angles between sugars associated with one base pair, and (iv) the observation that successive base planes in purine-pyrimidine steps open up the angle between them toward the major groove, whereas pyrimidine-purine steps open toward the minor groove. These features offer the beginning of an understanding of the way in which specific base sequences can perturb the structure of a B-DNA double helix so as to be "read" by intercalating drugs, repressors, and other recognition proteins.
mesh_terms: D001483:Base Sequence; D004247:DNA; D007364:Intercalating Agents; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D012097:Repressor Proteins; D013329:Structure-Activity Relationship; D014961:X-Ray Diffraction
chemical_list: D007364:Intercalating Agents; D009838:Oligodeoxyribonucleotides; D012097:Repressor Proteins; D004247:DNA