DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation.
Helical-twist, roll and torsion-angle variations calculated by the Calladine (1982)-Dickerson (1983) rules were scanned along several nucleotide sequences for which DNAase I cleavage data are available. It has been shown that for short synthetic oligomers DNAase I cuts preferentially at positions of high helical twist (Dickerson & Drew, 1981; Lomonossoff et al., 1981). Our calculations indicate that DNAase I sensitive and hypersensitive sites in chromatin are correlated with regions of successive, large, helical-twist angle variations from regular B-DNA. In many cases these regions exhibit large variations in base-pair roll and backbone torsion angles as well. It has been suggested that DNAase I cuts in the vicinity of cruciforms. However, it was recently demonstrated by Courey & Wang (1983) and Gellert et al. (1983) that such cruciform formation in a negatively supercoiled DNA is kinetically forbidden under physiological conditions. We thus propose that clustering of large twist-angle (and/or roll and backbone torsion angle) variations may be among the conformational features recognized by the enzyme. Specific cuts can then preferentially occur at base-pair steps with high helical twists.
D000818:Animals; D001483:Base Sequence; D002645:Chickens; D002843:Chromatin / Q000032:analysis; D004247:DNA / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D003850:Deoxyribonuclease I; D004330:Drosophila; D005796:Genes; D005838:Genotype; D005914:Globins / Q000235:genetics; D009690:Nucleic Acid Conformation; D011120:Polyomavirus / Q000235:genetics; D013539:Simian virus 40 / Q000235:genetics
D002843:Chromatin; D004279:DNA, Viral; D005914:Globins; D004247:DNA; D003850:Deoxyribonuclease I