Abstract
Because of open problems in the relation between results obtained by relaxation experiments and molecular dynamics simulations on the B-A transition of DNA, relaxation measurements of the B-A dynamics have been extended to a wider range of conditions. Field-induced reaction effects are measured selectively by the magic angle technique using a novel cell construction preventing perturbations from cell window anisotropy. The kinetics was recorded for the case of poly[d(AT)] up to the salt concentration limit of 4.4 mM, where aggregation does not yet interfere. Now experimental data on the B-A dynamics are available for poly[d(AT)] at salt concentrations of 0.18, 0.73, 2.44 and 4.4 mM. In all cases, a spectrum of time constants is found, ranging from ~ 10 μs up to components approaching ~ 1 ms. The relatively small dependence of these data on the salt concentration indicates that electrostatic effects on the kinetics are not as strong as may be expected. The ethanol content at the transition center is a linear function of the logarithm of the salt concentration, and the slope is close to that expected from polyelectrolyte theory. The B-A transition dynamics was also measured in D2O at a salt concentration of 2.4 mM: the center of the transition is found at 20.0 mol/l H2O and at 20.1 mol/l D2O with an estimated accuracy of ± 0.1 mol/l; the spectrum of time constants at the respective transition centers is very similar. The experimental results are discussed regarding the data obtained by molecular dynamics simulations.
Highlights
Looking at molecular models of the B- and A-form DNA suggests that the transition between these well-ordered, right-handed double-helical structures (Saenger 1984) is a relatively simple rearrangement
The time constants observed for the B-A transition by relaxation measurements at reduced water activity are in a time range that may be expected from the time constants of usual stacking rearrangements in a usual aqueous environment
Because the overall activation barrier corresponds to a factor of ~ 104, the present results indicate that the main part of this barrier is not due to electrostatics
Summary
Looking at molecular models of the B- and A-form DNA suggests that the transition between these well-ordered, right-handed double-helical structures (Saenger 1984) is a relatively simple rearrangement. The molecular details of Band A-helix structures in crystals have been analyzed at high resolution (Egli et al 1998; Schneider et al 1998; Dickerson and Ng 2001; Ng and Dickerson 2002). Because addition of ethanol favors the A form and aggregation and precipitation of DNA, such reactions had to be avoided by reduction of the salt concentration. These are the general boundary conditions for experimental studies of the B-A transition in solution—obviously valid for studies of both the equilibrium and kinetics. The dynamics of the B-A transition could only be analyzed by the electric field jump technique
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