The mechanism of ion polarisation along DNA double helices

Abstract

The orientation curves of short DNA fragments induced by electric field pulses are measured with high time resolution and analysed by efficient deconvolution techniques. A small, but clearly detectable delay of the 'on-field' orientation can be described accurately by the superposition of two exponential processes with opposite amplitudes. The time constant of the faster process is around 10 ns and the slower one in the range 50-1000 ns depending upon the electric field strength and chain length of the DNA fragment. The relation between amplitudes and time constants observed for each curve corresponds exactly to that expected for a convolution of two processes, where the first process is without optical response and becomes detectable only via the optical response of the second process. These results indicate that the first process reflects the polarisation of the ion atmosphere required for the second process of the orientation. Measurements at different ion concentrations c demonstrate that the reciprocal time constant of the fast process is a linear function of c and thus is consistent with an association reaction. The association rate constant evaluated from this dependence according to a simple bimolecular reaction model is 8 X 10(9) M-1 s-1 for a 95 base-pair fragment and is consistent with binding of Na+ to the helix, a reaction close to the limit of diffusion control. The association rate constant is almost independent of the electric field strength E, while the dissociation rate constant k- strongly increases with E, indicating dissociation of ions at high E values. The data suggest a linear correlation between log(k-) and E2 corresponding to a reaction driven by a dipole change. The apparent dipole change evaluated from this dependence is in the order of magnitude estimated for an elementary step of ion dissociation at one end of the helices. The combined results obtained from the polarisation and the orientation mechanism can be explained by dissociation of surprisingly few counterions biased towards one end of the helices. The experimental data obtained for a 76 base-pair fragment are analogous to those for the 95 base-pair fragment, whereas the 'slow' ion polarisation has not been detected for a fragment with 27 base-pairs. This result together with those obtained for the longer fragments at low field strengths indicate that there is a fast polarisation mechanism without 'ion dissociation' at low chain lengths and for low electric field strengths. This mechanism is replaced at high chain lengths and/or high electric field strengths by the ion dissociation mechanism.(ABSTRACT TRUNCATED AT 400 WORDS)