Simulated and Experimental Bending Dynamics in DNA with and without A-Tracts

Abstract

The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of DNA structure. We report here the results of comparative theoretical and experimental studies of bending dynamics in 35-mer DNA fragments. This length appears large enough for the curvature to be distinguished by gel electrophoresis. Two DNA fragments, with identical base pair composition, but different sequences are compared. In the first one, a single A-tract motif was four times repeated in phase with the helical screw whereas the second sequence was "random". Both calculations and experiments indicate that the A-tract DNA is distinguished by the large static curvature and characteristic bending dynamics, suggesting that the computed effect corresponds to the experimental phenomenon. The results poorly agree with earlier views that attributed a decisive role in DNA bending to sequence specific base pair stacking or binding of solvent counterions, but lend additional support to the hypothesis of a compressed frustrated state of the backbone as the principal physical cause of the static curvature. We discuss the possible ways of experimental verification of this hypothesis.