Dynamics of the B–A transition of DNA double helices

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Oxford University Press

RESUMO

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 ∼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 ∼1600 bp are in the range around 10 µs. An additional process with time constants of ∼100 µs is probably due to nucleation. The same time constants (within experimental accuracy ±10%) were observed for a poly[d(A-T)] sample with ∼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.

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