Helical phasing between DNA bends and the determination of bend direction

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Abstract
The presence and location of bends in DNA can be inferred from the anomalous mobility of DNA fragments or protein-DNA complexes during electrophoresls in polyacrylamide gels. Direction of bending is not so easily determined. We show here that a protein-induced bend, when linked to a protein-independent DNA bend by a segment of variable length, exhibits an electrophoretic mobility that varies in a sinusoidal manner with the length of the linker. Mobility minima occur once for each addition to the linker of one helical turn of DNA. Since minima should occur when two bends reinforce one another, the direction of one bend relative to the other can be determined from the distances between the two centers of bending at which minima occur. Our results strongly support the idea that the A5-6 tracts in kinetoplast DNA bend towards the minor groove while the bend at the recombination site of the γδ resolvase (binding site I of the 76 res site) bends towards the major groove.