DNA structural variations in the E. coli tyrT promoter.
X-ray studies have established that the structure of a right-handed, Watson-Crick double helix can change from place to place along its length as a function of base sequence. The base pairs transmit deformations out to the phosphate backbone, where they can then be recognized by proteins and other DNA-binding reagents. Here we have examined at single-bond resolution the interactions of three commonly used nucleases (DNAase I, DNAase II, and copper-phenanthroline) with a DNA of natural origin, the 160 bp tyrT promoter. All three of these reagents seem sensitive to DNA backbone geometry rather than base sequence per se. Their sequence-dependent patterns of cleavage provide evidence for structural polymorphism of several sorts: global variation in helix groove width, global variation in radial asymmetry, and local variation in phosphate accessibility. These findings explain how sequence zones of a certain base composition, or purine-pyrimidine asymmetry, can influence the recognition of DNA by protein molecules.
D001483:Base Sequence; D004262:DNA Restriction Enzymes; D004269:DNA, Bacterial / Q000235:genetics*; D003851:Deoxyribonucleases; D004121:Dimethyl Sulfoxide / Q000494:pharmacology; D004926:Escherichia coli / Q000235:genetics*; D005798:Genes, Bacterial; D014644:Genetic Variation; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D009876:Operon; D012346:RNA, Transfer, Amino Acyl / Q000235:genetics*; D013696:Temperature
D004269:DNA, Bacterial; D012346:RNA, Transfer, Amino Acyl; D003851:Deoxyribonucleases; D004262:DNA Restriction Enzymes; D004121:Dimethyl Sulfoxide