Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.

TitleBinding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.
Publication TypeJournal Article
Year of Publication2007
AuthorsOrtega, José-Antonio, Blas José Ramón, Orozco Modesto, Grandas Anna, Pedroso Enrique, and Robles Jordi
JournalOrg Lett
Volume9
Pagination4503-6
Date Published2007 Oct 25
ISSN1523-7060
KeywordsBase Sequence, Cytosine, Nucleic Acid Conformation, Oligonucleotides, Oxazines, Peptide Nucleic Acids
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.
DOI10.1021/ol701826x