Detection of localized DNA flexibility

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Abstract
The bending and flexibility of DNA are important in packaging, recombination and transcription. Bending decreases electrophoretic mobility in a manner depending on bend position within a fragment (circular permutation) and on the distance between bends (phasing analysis). Bending can also affect DNA ring closure (cyclization). The lack of a complete theory for the mechanism of gel retardation hampers measurement of bend magnitudes by electrophoresis, whereas cyclization is done entirely in solution and is well understood theoretically. Disagreements between bend angles estimated by the two electrophoretic assays have been ascribed to DNA flexibility. Here we test this interpretation using an internal loop as a model flexible locus. Whereas the circular permutation and helical phasing experiments are only subtly affected by the loop, DNA cyclization kinetics detects and quantifies substantial increases in torsional and bending flexibility. Furthermore, the results support a functional role for the stress of DNA bending in inducing base-pair opening.