title: Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules.
abstract: Oligonucleotides containing 5-(N-aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA, oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine ((N)U) or 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine ((N)U(m)), respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand the structural implications of (N)U and (N)U(m) substitutions, we have determined the X-ray crystal structures of DNA:DNA duplexes containing either (N)U or (N)U(m) and of DNA:RNA hybrid duplexes containing (N)U(m). The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to (N)U, (N)U(m) decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the (N)U(m) containing DNA:DNA duplex structure. The conformation of (N)U(m), however, is compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore, the ability of (N)U(m) to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity.
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
authors.forename: Ella Czarina Magat
authors.initials: EC
authors.lastname: Juan
authors.forename: Jiro
authors.initials: J
authors.lastname: Kondo
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kurihara
authors.forename: Takanori
authors.initials: T
authors.lastname: Ito
authors.forename: Yoshihito
authors.initials: Y
authors.lastname: Ueno
authors.forename: Akira
authors.initials: A
authors.lastname: Matsuda
authors.forename: Akio
authors.initials: A
authors.lastname: Takénaka
mesh_terms: D002236:Carbohydrate Conformation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D044704:DNA, A-Form / Q000737:chemistry; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D016376:Oligonucleotides, Antisense / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: C474860:5-(N-aminohexyl)carbamoyl-2'-O-methyluridine; C108707:5-(N-aminohexyl)carbamoyl-2'-deoxyuridine; D044704:DNA, A-Form; D009841:Oligonucleotides; D016376:Oligonucleotides, Antisense; D012313:RNA; D004247:DNA; D003857:Deoxyuridine; D014529:Uridine