title: Influence of DNA sequence and supercoiling on the process of cruciform formation.
abstract: We have studied some of the effects of DNA sequence and negative superhelicity on the rate of cruciform formation. Replacing the sequence AATT at the center of a perfect 68 base-pair palindromic sequence with the sequence CCCGGG decreases the rate of cruciform formation by a factor of at least 100. The logarithm of the rate constant of cruciform formation was found to increase linearly with linking difference. For the 68 base-pair perfect palindrome in a 4400 base-pair plasmid, each additional negative superhelical turn increased the rate of cruciform formation by a factor of 1.6. These results are consistent with a mechanism in which cruciform formation is initiated by the formation of a single-stranded bubble, 10 base-pairs in length, near the center of the palindromic sequence. In addition, we have examined the effect of introducing an asymmetric insertion into the palindromic sequence.
authors.affiliation: Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138.
authors.forename: A J
authors.initials: AJ
authors.lastname: Courey
authors.forename: J C
authors.initials: JC
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D004278:DNA, Superhelical; D004587:Electrophoresis, Agar Gel; D007700:Kinetics; D009690:Nucleic Acid Conformation; D010957:Plasmids
chemical_list: D004278:DNA, Superhelical