Structures of the potassium-saturated, 2 : 1, and intermediate, 1 : 1,forms of a quadruplex DNA

Potassium can stabilize the formation of chair- or edge-type quadruplex DNA structures and appears to be the only naturally occurring cation that can do so. As quadruplex DNAs may be important in the structure of telomere, ce ntromere, triplet repeat and other DNAs, information about the details of t he potassium-quadruplex DNA interactions are of interest. The structures of the 1 :1 and the fully saturated, 2:1, potassium-DNA complexes of d(GGTTGG TGTGGTTGG) have been determined using the combination of experimental NMR r esults and restrained molecular dynamics simulations, The refined structure s have been used to model the interactions at the potassium binding sites. Comparison of the 1:1 and 2:1 potassium:DNA structures indicates how potass ium binding can determine the folding pattern of the DNA, In each binding s ite potassium interacts with the carbonyl oxygens of both the loop thymine residues and the guanine residues of the adjacent quartet.