Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.
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.
Ortega
José-Antonio
JA
Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain.
Blas
José Ramón
JR
Orozco
Modesto
M
Grandas
Anna
A
Pedroso
Enrique
E
Robles
Jordi
J
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*
C470812:9-(2-aminoethoxy)phenoxazine; D009841:Oligonucleotides; D010078:Oxazines; D020135:Peptide Nucleic Acids; D003596:Cytosine; C039203:phenoxazine