Detection of DNA Bending by Gel Electrophoresis: Use of Plasmid Vectors

Abstract

Bend in a segment of the DNA backbone, whether intrinsic or induced by binding of a sequence-specific protein, helps formation of DNA-multiprotein complexes; DNA-protein or protein-protein contact required for biologically effective compaction of the complexes is facilitated. Such bending can be easily monitored by gel electrophoresis, making use of the change in electrophoretic mobility of a contorted DNA fragment. The mobility varies according to the site and degree of bending (Wu and Crothers, 1984) ; a bend in the middle of the DNAfragment reduces the mobility more than a bend at either end. For analysis of DNA bending using change in mobility, the DNA sequence is inserted at one cloning site of a plasmid vector carrying two identical DNA segments with many restriction sites in a direct repeat spanning a central region containing the cloning sites (Kim et al., 1989).