DETECTION OF LOCALIZED DNA FLEXIBILITY

THE bending and flexibility of DNA are important in packaging, recombi nation and transcription(1-3). Bending decreases electrophoretic mobil ity in a manner depending on bend position within a fragment (circular permutation(4)) and on the distance between bends (phasing analysis(5 ,6)). Bending can also affect DNA ring closure (cyclization(7-10)). Th e lack of a complete theory for the mechanism of gel retardation hampe rs measurement of bend magnitudes by electrophoresis, whereas cyclizat ion is done entirely in solution and is well understood theoretically( 9). Disagreements between bend angles estimated by the two electrophor etic assays have been ascribed to DNA flexibility(11). Here we test th is interpretation using an internal loop as a model flexible locus. Wh ereas the circular permutation and helical phasing experiments are onl y subtly affected by the loop, DNA cyclization kinetics detects and qu antifies substantial increases in torsional and bending flexibility. F urthermore, the results support a functional role for the stress of DN A bending in inducing base-pair opening(12).