EVIDENCE FOR THE STOCHASTIC NATURE OF BASE PAIR OPENING IN DNA - A BROWNIAN DYNAMICS SIMULATION

The time dependence of the opening of the central thymine base in a B-DNA (dA)5.(dT)5 oligomer has been simulated by Brownian dynamics using a previously developed opening model where the base is allowed to rotate toward the major groove of the double helix around an axis perpendicular to the base plane and passing roughly through the center of the sugar moiety. From an analysis of the considerable variations of this rotation angle as a function of time, it is possible to estimate the lifetime of the base pair as well as the activation energy for the opening process. These values are found to be in good agreement with the corresponding experimental measurements obtained by hydrogen exchange. This study thus points to the stochastic character of the base pair opening process in double-stranded nucleic acids.