5′-Peptidyl substituents allow a tuning of the affinity of oligodeoxyribonucleotides for RNA

The affinity of amide-linked 5′-aminoacyl and 5′-dipeptidyl DNA octamers for two RNA undecamers with 3′-overhangs was measured via UV melting analysis. A sequence-dependent increase in melting points was observed. At low ionic strength, two appended lysine residues elevate melting points more than two additional A:U base pairs. The stability of duplexes between amide-linked 5′-aminoacyl- and 5′-dipeptidyl DNA octamers and RNA undecamers was determined in UV melting experiments. A sequence-dependent increase of affinity was found, with ΔTms ranging from +21 °C for a dilysinyl substituent at 10 mM salt concentration to +1 °C for a tryptophanyl residue at 150 mM salt concentration.