Abstract

The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na+ solution hasbeen determined using molecular dynamics calculations constrained by distance and dihedral restraintsderived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimerof dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:Amismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composedof alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymineintersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture haspotential implications in genetic recombination. It suggests a pathway for oligomerization involvingassociation of quadruplex entities through GpC steps.