Amide backbone modifications for antisense oligonucleotides carrying potential intercalating substituents: Influence on the thermodynamic stability of the corresponding duplexes with RNA- and DNA- complements

The synthesis of the amide dimers 3–5 carrying a potential intercalating substituent on the nitrogen atom of the backbone is presented, together with the incorporation of these modifications into oligonucleotides, the resulting melting temperatures (Tmʹs) of the corresponding duplexes with RNA- and DNA- complements, and a summary of molecular modeling studies.