AN IMPROVED METHOD FOR THE RAPID ASSESSMENT OF DNA BENDING BY SMALL MOLECULES

Assessing the effects of non-covalently bound chemicals on DNA structu re is particularly challenging. Traditional methods require the use of cumbersome electrophoretic techniques or that the compounds bind DNA with an extremely high affinity. Here we demonstrate that, by extendin g the use of the exonuclease Bal 31, we can rely on a standard cycliza tion assay technique and one dimensional gel electrophoresis to identi fy and quantitate chemical induced DNA bending. An important applicati on of this method is to the study of small molecules that bind to DNA non-covalently and we illustrate the method with the antitumor antibio tic calicheamicin. Our results suggest that the distribution of circle s resulting from the polymerization of a 21 bp DNA construct reflects the kinetics of the competing cyclization and dimerization reactions a nd provides a method for rapidly screening compounds for DNA bending.