Single-stranded breaks relax intrinsic curvature in DNA?

The recent hypothesis of a compressed backbone state as the origin of the intrinsic curvature in DNA suggested that it could result from a geometric mismatch between the partial specific backbone length and optimal base stacking. It predicted that the long-known phenomenon of static curvature in A-tract repeats may be affected by single-stranded breaks (nicks) that should relax it in a position-dependent manner. To check the aforementioned prediction, a special series of nicked DNA fragments was prepared from two mother sequences, one including phased A-tract repeats and the other being random, and the curvature was probed experimentally by gel mobility assays. In agreement with earlier reports, single-stranded breaks produce virtually no effect upon the gel mobility of the random sequence DNA. In contrast, for nicked A-tract fragments, the curvature exhibits regular periodical behavior depending upon the position of the strand break with respect to the overall bend. The modulations are rather strong, with the maximal increase in gel mobility exceeding 30% of the initial difference with respect to the reference straight DNA. This effect has not been encountered before, and it is opposite the usual nonspecific retardation caused by single-stranded breaks. The amplitude of the observed modulation is increased for phosphorylated nicks and in the presence of Mg(2+) ions.