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 TC 18 repeat and on one half of the AG 18 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 p H and the degree of negative supercoiling: at p H 7.6 to 7.7, a high level of supercoiling was needed to keep about half of the molecules in the H conformation; at p H 6 and p H 5, normal levels of supercoiling supported H-DNA; and at p H 4, no supercoiling was required. At mildly alkaline p H, 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.