A dimeric DNA interface stabilized by stacked A center dot(G center dot G center dot G center dot G)center dot A hexads and coordinated monovalent cations

We report on the identification of an A.(G.G.G.G) A hexad pairing alignment which involves recognition of the exposed minor groove of opposing guanine s within a G.G.G.G tetrad through sheared G.A mismatch formation. This unex pected hexad pairing alignment was identified for the d(G-G-A-G-G-A-G) sequ ence in 150 mM Na+ (or K+) cation solution where four symmetry-related stra nds align into a novel dimeric motif. Each symmetric half of the dimeric "h exad" motif is composed of two strands and contains a stacked array of an A .(G.G.G.G) A hexad, a G.G.G.G tetrad, and an A.A mismatch. Each strand in t he hexad motif contains two successive turns, that together define an S-sha ped double chain reversal fold, which connects the two G-G steps aligned pa rallel to each other along adjacent edges of the quadruplex. Our studies al so establish a novel structural transition for the d(G-G-A-G-G-A-N) sequenc e, N = T and G, from an "arrowhead" motif stabilized through cross-strand s tacking and mismatch formation in 10 mM Na+ solution (reported previously), to a dimeric hexad motif stabilized by extensive inter-subunit stacking of symmetry-related A.(G G-G G).A hexads in 150 mM Na+ solution. Potential mo novalent cation binding sites within the arrowhead and hexad motifs have be en probed by a combination of Brownian dynamics and unconstrained molecular dynamics calculations. We could not identify stable monovalent cation-bind ing sites in the low salt arrowhead motif. BY contrast, five electronegativ e pockets were identified in the moderate salt dimeric hexad motif. Three o f these are involved in cation binding sites sandwiched between G.G.G.G tet rad planes and two others, are involved in water-mediated cation binding si tes spanning the unoccupied grooves associated with the adjacent stacked A. (G.G.G.G).A hexads. Our demonstration of A.(G.G.G.G).A hexad formation open s opportunities for the design of adenine-rich G-quadruplex-interacting oli gomers that could potentially target base edges of stacked G.G.G.G tetrads. Such an approach could complement current efforts to design groove-binding and intercalating ligands that target G-quadruplexes in attempts designed to block the activity of the enzyme telomerase. (C) 2000 Academic Press.