title: X-ray structure of d(GCGAAGC); switching of partner for G:A pair in duplex form.
abstract: 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.
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: Masaru
authors.initials: M
authors.lastname: Tsunoda
authors.forename: Takeshi
authors.initials: T
authors.lastname: Sekiguchi
authors.forename: Ichiro
authors.initials: I
authors.lastname: Hirao
authors.forename: Kimitsuna
authors.initials: K
authors.lastname: Watanabe
authors.forename: Kin-ichiro
authors.initials: K
authors.lastname: Miura
authors.forename: Akio
authors.initials: A
authors.lastname: Takénaka
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA