title: Crystal structure of d(GCGAAAGCT) containing parallel-stranded duplex with homo base pairs and anti-parallel duplex with Watson-Crick base pairs.
abstract: A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized under a slightly acidic condition, and its crystal structure has been determined at 2.5A resolution. In the first half of the oligomer, the sequence CGAA forms a parallel duplex with another symmetry-related half through the homo base pairs, C2:C2+ (semi-protonated between the Watson-Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The second halves of the parallel duplex are split away in the different direction, and extended to form an anti-parallel B-form duplex with another second half.
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: Tomonori
authors.initials: T
authors.lastname: Kobuna
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: K
authors.lastname: Miura
authors.forename: Akio
authors.initials: A
authors.lastname: Takénaka
mesh_terms: D020029:Base Pairing; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA