Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.
|Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.
|Year of Publication
|Ortega, José-Antonio, Blas José Ramón, Orozco Modesto, Grandas Anna, Pedroso Enrique, and Robles Jordi
|2007 Oct 25
|Base Sequence, Cytosine, Nucleic Acid Conformation, Oligonucleotides, Oxazines, Peptide Nucleic Acids
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.