Disruptions of the Regular Structure in DNA Minicircles

Abstract

DNA bending and torsional deformations, which often occur during its functioning inside the cell, can cause local disruptions of the regular helical structure. The disruptions created by negative torsional stress have been studied in detail, but those caused by bending stress have only been analyzed theoretically. To address the problem, we probed the structure of very small DNA circles, 63 - 105 bp in length, by single-strand-specific endonucleases. We determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm. The experimental data suggest that strong DNA bending initiates kink formation while preserving base pairing. To get quantitative information about the disruptions we developed a statistical-mechanical model of the disruption formations in DNA minicircles. The model, used in the computer simulation, specifies the disruptions by three parameters: DNA bend angle at the disruption θd, local DNA unwinding caused by the disruption formation, and the free energy associated with the disruption formation in unstressed double helix, Gd. We obtained a relationship between values of Gd and θd under which the theoretical results are compatible with the experimental data. The relationship suggests that the free energy of a base pair opening, which includes flipping out both bases, is significantly higher than the generally accepted value.