Interaction of a G-DNA quadruplex with mono- and divalent cations. A force field calculation.
The formation and stability of four-stranded DNA in solution is specifically dependent on the type of cations present. The interaction potential of a model quadruplex structure with different mono- and divalent ions was determined by force field calculations. Though the electrostatic contribution to the total energy is mainly responsible for the stabilisation of the cations within the quadruplex channel, it is the van der Waals interaction at short distances that determines the specific characteristics of the different cations. An explicit consideration of the solvent indicates that the position of water molecules in close proximity to the DNA channel have a strong influence on the form of the potential, and hence on the capability of the cations for leaving and re-entering the cavity. The effect of cation size, as expressed through their Lennard-Jones parameters, is discussed.
Töhl
J
J
Department of Chemistry, University of Bielefeld, PO. Box 10 01 31, D-33 501 Bielefeld, Germany.
Eimer
W
W