title: Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.
abstract: Melting temperatures of DNA duplexes containing the phenoxazine (P) and G-clamp (X) cytosine analogues exhibited a strong and unusual dependence on the nucleoside flanking the modified nucleobase, and the same trend was observed in PNA-DNA duplexes incorporating X in the PNA chain. Molecular dynamics simulations of the DNA duplexes show that generalized stacking (including secondary interactions of the ammonium group of X) and hydrogen bonding are good descriptors of the different duplex stabilities.
authors.affiliation: Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain.
authors.forename: José-Antonio
authors.initials: JA
authors.lastname: Ortega
authors.forename: José Ramón
authors.initials: JR
authors.lastname: Blas
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.forename: Anna
authors.initials: A
authors.lastname: Grandas
authors.forename: Enrique
authors.initials: E
authors.lastname: Pedroso
authors.forename: Jordi
authors.initials: J
authors.lastname: Robles
mesh_terms: D001483:Base Sequence; D003596:Cytosine / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D010078:Oxazines / Q000737:chemistry*; D020135:Peptide Nucleic Acids / Q000737:chemistry*
chemical_list: C470812:9-(2-aminoethoxy)phenoxazine; D009841:Oligonucleotides; D010078:Oxazines; D020135:Peptide Nucleic Acids; D003596:Cytosine; C039203:phenoxazine