An improved method for the rapid assessment of DNA bending by small molecules

Assessing the effects of non-covalently bound chemicals on DNA structure 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 extending the use of the exonuclease Bal 31, we can rely on a standard cyclization assay technique and one dimensional gel electrophoresis to identify and quantitate chemical induced DNA bending. An important application of this method is to the study of small molecules that bind to DNA non-covalently and we illustrate the method with the antitumor antibiotic calicheamicin. Our results suggest that the distribution of circles resulting from the polymerization of a 21 bp DNA construct reflects the kinetics of the competing cyclization and dimerization reactions and provides a method for rapidly screening compounds for DNA bending.