title: Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
abstract: The incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3-4 K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights 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 1.9-2.9 Å resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson-Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5'-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization.
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
authors.forename: Ella Czarina
authors.initials: EC
authors.lastname: Magat Juan
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: Tsuyoshi
authors.initials: T
authors.lastname: Haraguchi
authors.forename: Fang
authors.initials: F
authors.lastname: Zhang
authors.forename: Masaru
authors.initials: M
authors.lastname: Tsunoda
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: D020029:Base Pairing; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: C520055:7,8-dihydropyrido(2,3-d)pyrimidin-2-one; D005456:Fluorescent Dyes; D003596:Cytosine; D004247:DNA