Sequence-dependent kinks induced in curved DNA.

In certain curved DNA fragments without AA dinucleotides, the gel retardation anomaly associated with curvature passes through a maximum with fragment length, indicating length (and electric field) dependent structural transitions in the DNA. We suggest that thermally induced stereochemical kinks in DNA are stabilized in the gel, thus relieving the effects of curvature. These kinks are shown to occur specifically at CA/TG and TA/TA stacks. Other physical and biological evidence points to frequent structural dislocations at CA and TA steps. These reversible sequence dependent kinks may therefore represent a novel class of structural protein-DNA recognition elements.