Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure

A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson-Crick G·C base pairs and a subsequent sheared G·A pair at both ends. The central two A residues are free from base-pair formation. The corresponding base moieties of the two strands are intercalated and stacked on each other, forming a long column of G₁-C₂-G₃-A₄-A-A₅-A-G-C-G (asterisks indicate the counter-strand). The Watson-Crick and major-groove sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to those found in the nonamers d(G^BrCGAAAGCT) and d(G^ICGAAAGCT), the base-intercalated duplex may be a stable form of the specific sequence. Electrophoresis results suggest that the octamer has two states, monomeric and dimeric, in solution depending on the Mg²⁺ concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions.