title: Single strands, triple strands, and kinks in H-DNA.
abstract: A naturally occurring (dT-dC)18:(dA-dG)18 repeat in the H conformation of DNA was shown to contain single-stranded nucleotides in the center of the TC18 repeat and on one half of the AG18 repeat. These results support the model that H-DNA is a structure containing both triple-stranded and single-stranded regions. The stability of this structure was affected by both pH and the degree of negative supercoiling: at pH 7.6 to 7.7, a high level of supercoiling was needed to keep about half of the molecules in the H conformation; at pH 6 and pH 5, normal levels of supercoiling supported H-DNA; and at pH 4, no supercoiling was required. At mildly alkaline pH, the TC/AG18 repeat assumed a novel conformation called J-DNA that differed from both the B and H forms. A three-dimensional model for the structure of H-DNA is proposed that accounts both for the single-strandedness of the nucleotides and for the influence of supercoiling on H-DNA formation. This model predicts and evidence is presented that H-DNA introduces a sharp kink in the DNA. Moreover, the angle of this kink appears not to be fixed, so that H-DNA is also a hinged-DNA.
authors.affiliation: Department of Physiological Chemistry, University of Wisconsin-Madison 53706.
authors.forename: H
authors.initials: H
authors.lastname: Htun
authors.forename: J E
authors.initials: JE
authors.lastname: Dahlberg
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000648:ultrastructure*; D004277:DNA, Single-Stranded / Q000648:ultrastructure; D004278:DNA, Superhelical; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation
chemical_list: D004277:DNA, Single-Stranded; D004278:DNA, Superhelical; D004247:DNA