title: Crystal structures of DNA duplexes stabilized by bicyclic-C residues.
abstract: Chemical modification of nucleic acids is being studied extensively as an approach for the development of nucleic acid-based therapies. We found that a nucleotide carrying 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (bicyclic-C or X), which is a cytosine derivative with a propene attached at the N4 and C5 atoms, increases the stability of DNA duplexes. To establish the conformational effects of X on DNA and to obtain insight into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)](2) and [d(CGCGAAT-X-CGCG)](2) have been determined at 2.9 A resolutions. In both duplexes, the bicyclic-C bases form pairs with the counter bases through hydrogen bonds, and stabilize the duplex formation in part by stacking interactions between X and the subsequent thymine base of the same strand.
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Haraguchi
authors.forename: Satoru
authors.initials: S
authors.lastname: Shimizu
authors.forename: Xiao
authors.initials: X
authors.lastname: Ma
authors.forename: Taizo
authors.initials: T
authors.lastname: Kurose
authors.forename: Ella Czarina Magat
authors.initials: EC
authors.lastname: Juan
authors.forename: Akihiro
authors.initials: A
authors.lastname: Ohkubo
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
authors.forename: Takayuki
authors.initials: T
authors.lastname: Shibata
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Millington
authors.forename: David M
authors.initials: DM
authors.lastname: Williams
authors.forename: Akio
authors.initials: A
authors.lastname: Takénaka
mesh_terms: D020137:Base Pair Mismatch; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: C520055:7,8-dihydropyrido(2,3-d)pyrimidin-2-one; D003596:Cytosine; D004247:DNA