Relating independent measures of DNA curvature: Electrophoretic anomaly and cyclization efficiency

Electrophoretic methods are often used to measure DNA curvature and protein -induced DNA bending. Though convenient and widely-applied, quantitative an alyses are generally limited to assays for which empirical calibration stan dards have been developed. Alternatively solution-based cyclization of shor t DNA duplexes allows analysis of DNA curvature and bending from first prin ciples, but a detailed understanding of this assay is still lacking. In thi s work, we demonstrate that calibration with an independent electrophoretic assay of DNA curvature permits interpretation of cyclization assay results in a quantitatively meaningful way. We systematically measure intrinsic DN A curvature in short duplexes using a well-established empirical ligation l adder assay. We then compare the results to those obtained from the analysi s of the distribution of circular products obtained in simple enzymatic cyc lization assays of the same duplexes when polymerized. A strong correlation between DNA curvature estimates from these two assays is obtained for DNA fragments between 150-300 bp in length. We discuss how this result might be used to improve quantitative analysis of protein-mediated bending events e valuated by cyclization methods. Our results suggest that measurements of D NA curvature obtained under similar conditions, in solution and in an acryl amide gel matrix, can be compared directly. The ability to correlate result s of these simple assays may prove convenient in monitoring DNA curvature a nd flexibility.