title: Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure.
abstract: 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 G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*) (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(Br)CGAAAGCT) and d(G(I)CGAAAGCT), 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 Mg(2+) concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions.
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Sunami
authors.forename: Jiro
authors.initials: J
authors.lastname: Kondo
authors.forename: Ichiro
authors.initials: I
authors.lastname: Hirao
authors.forename: Kimitsuna
authors.initials: K
authors.lastname: Watanabe
authors.forename: Kin Ichiro
authors.initials: KI
authors.lastname: Miura
authors.forename: Akio
authors.initials: A
authors.lastname: Takénaka
mesh_terms: D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D007364:Intercalating Agents / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D007364:Intercalating Agents; D009841:Oligonucleotides; D004247:DNA