Dynamics of the B-A transition of DNA double helices

Although the transition from the B-DNA double helix to the A-form is essential for biological function, as shown by the existence of the A-form in many protein-DNA complexes, the dynamics of this transition has not been resolved yet. According to molecular dynamics simulations the transition is expected in the time range of a few nanoseconds. The B-A transition induced by mixing of DNA samples with ethanol in stopped flow experiments is complete within the deadtime, showing that the reaction is faster than approximately 0.2 ms. The reaction was resolved by an electric field jump technique with induction of the transition by a dipole stretching force driving the A- to the B-form. Poly[d(A-T)] was established as a favourable model system, because of a particularly high cooperativity of the transition and because of a spectral signature allowing separation of potential side reactions. The time constants observed in the case of poly[d(A-T)] with approximately 1600 bp are in the range around 10 micros. An additional process with time constants of approximately 100 micros is probably due to nucleation. The same time constants (within experimental accuracy +/-10%) were observed for a poly[d(A-T)] sample with approximately 70 bp. Under low salt conditions commonly used for studies of the B-A transition, the time constants are almost independent of the ionic strength. The experimental data show that a significant activation barrier exists in the B-A transition and that the helical states are clearly separated from each other, in contrast to predictions by molecular dynamics simulations.