X-ray structure of d(GCGAAGC); switching of partner for G:A pair in duplex form.

Crystal structure of a DNA fragment d(GCGAAGC), known to adopt a stable mini-hairpin structure in solution, has been determined at 1.6A resolution. Two heptamers are associated to form a duplex with a molecular two-fold symmetry. Three duplexes in the asymmetric unit have a similar structure. At the both ends of each duplexes, two Watson-Crick G:C pairs constitute the stem region. In the central part, two sheared pairs of G:A and A:G are formed, the two G bases being stacked as well as the two A bases. At this point, the two strands are crossed between the two base-stacked columns. The adenine moiety of the bulged A5 residue, which intercalates between the A4 and G6 residues, makes a small bending of the duplex at the two sites. The difference between the bulge-in structure of d(GCGAAGC) and the zipper-like duplex of d(GCGAAAGC) is ascribed to switching the partner of the sheared G:A pairs.