title: Chemical probing of the B-Z transition in negatively supercoiled DNA.
abstract: An analysis of the B-to-Z transition as a function of supercoiling for a natural Z-DNA-forming sequence found in plasmid pBR322 is presented at nucleotide resolution. The analysis is based on reactivity to four chemical probes which exhibit hyperreactivity in the presence of Z-DNA: hydroxylamine, osmium tetroxide, diethyl pyrocarbonate and dimethyl sulfate. We find that the initial transition occurs largely within a 14 base pair region which is mostly alternating purines and pyrimidines. With increasing negative supercoiling. Z-DNA extends into flanking regions having less and less alternating character, first one direction and then in the other. Evidence of B-Z junctions is seen at four sites bracketing these three adjacent regions. One of these Z-forming regions contains the non-alternating sequence CTCCT, suggesting that such sequences can form Z-DNA without great difficulty if they are adjacent to alternating sequences. A plasmid containing three copies of a 61 base pair fragment bearing the entire Z-forming region shows equal reactivity of all three copies at any given superhelical density, implying that they compete equally and independently for the torsional strain energy which promotes the B-Z transition, and are unaffected by adjacent sequences more than 20-30 base pairs away.
authors.affiliation: Department of Biology Massachusetts Institute of Technology Cambridge 02139.
authors.forename: B H
authors.initials: BH
authors.lastname: Johnston
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004278:DNA, Superhelical / Q000032:analysis; D004047:Diethyl Pyrocarbonate; D006898:Hydroxylamines; D008969:Molecular Sequence Data; D009993:Osmium Tetroxide; D010957:Plasmids; D013463:Sulfuric Acid Esters
chemical_list: D004278:DNA, Superhelical; D006898:Hydroxylamines; D013463:Sulfuric Acid Esters; C007482:dimethyl sulfate; D004047:Diethyl Pyrocarbonate; D009993:Osmium Tetroxide