DNA bend direction by phase sensitive detection

Abstract

Gel electrophoresis of DNA and protein-DNA complexes has been a key method used in studies of sequence-directed and protein-induced DNA bending. Natural DNA sequences can have protein binding sites adjacent to A-tract bending sites, resulting in the potential for the formation of topologically complex shapes in a localized DNA regulatory domain. An essential first step in deducing the structure and functional significance of such domains is elucidation of the relative direction of bending, which can be determined from the electrophoretic mobilities of isomers having varied helical phasing between the bends. Taking DNA bent around CAP protein as a standard, we conclude that the junction bending model correctly predicts the direction of bending at A tracts in kinetoplast DNA. The overall direction of the bend is towards the minor groove at the centre of the A tract.