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

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Porschke,  D.
Research Group of Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Citation

Porschke, D. (2016). Boundary conditions for free A-DNA in solution and the relation of local to global DNA structures at reduced water activity. European Biophysics Journal, 45(5), 413-421. doi:10.1007/s00249-015-1110-1.


Cite as: http://hdl.handle.net/11858/00-001M-0000-002A-E764-7
Abstract
Because of repeated claims that A-DNA cannot exist without aggregation or condensation, the state of DNA restriction fragments with 84-859bp has been analyzed in aqueous solutions upon reduction of the water activity. Rotational diffusion times tau (d) measured by electric dichroism at different water activities with a wide variation of viscosities are normalized to values tau (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 ≤1mM. The aggregation boundary, indicated by a strong increase of tau (c), is shifted to higher monovalent salt (≥4mM) when ethanol is replaced by trifluoroethanol. The BA transition is not indicated anymore by a cooperative change of tau (c) for [Formula: see text]p; tau (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.