Boundary conditions for free A-DNA in solution and the relation of local to global DNA structures at reduced water...

Because of repeated claims that A-DNA cannot exist without aggregation or condensation, the state of DNA restriction fragments with 84-859 bp has been analyzed in aqueous solutions upon reduction of the water activity. Rotational diffusion times τ (d) measured by electric dichroism at different water activities with a wide variation of viscosities are normalized to values τ (c) at the viscosity of water, which indicate DNA structures at a high sensitivity. For short helices (chain lengths [Formula: see text] ≤ persistence length p), cooperative formation of A-DNA is reflected by the expected reduction of the hydrodynamic length; the transition to the A-form is without aggregation or condensation upon addition of ethanol at monovalent salt ≤1 mM. The aggregation boundary, indicated by a strong increase of τ (c), is shifted to higher monovalent salt (≥4 mM) when ethanol is replaced by trifluoroethanol. The BA transition is not indicated anymore by a cooperative change of τ (c) for [Formula: see text] » p; τ (c) values for these long chains decrease upon reduction of the water activity continuously over the full range, including the BA transition interval. This suggests a non-cooperative BC transition, which induces DNA curvature. The resulting wide distribution of global structures hides changes of local length during the BA transition. Free A-DNA without aggregation/condensation is found at low-salt concentrations where aggregation is inhibited and/or very slow. In an intermediate range of solvent conditions, where the A-form starts to aggregate, a time window remains that can be used for analysis of free A-DNA in a quasi-equilibrium state.