Abstract
The easily accessible C-nucleoside 2-amino-5-(2‘-deoxy-β-d-ribofuranosyl)pyridine (P) and its 3-methyl (MeP) and 2‘-O-methyl (POMe) derivatives were synthesized and incorporated as protonated cytidine equivalents in homopyrimidine oligodeoxynucleotides. Tm measurements indicate that oligonucleotides containing P or MeP have a higher affinity to double-stranded DNA over the pH range of 6−8 than 5-methylcytidine (MeC) containing oligonucleotides. This increase in stability is most pronounced above pH 7.0. The average increase in Tm/modification for the dissociation of oligonucleotide d(TTTTTMePTMePTMePTMePTMePT) from a 21-mer target duplex at pH 7.5 is 2.3 °C relative to oligonucleotide d(TTTTTMeCTMeCTMeCTMeCTMeCT). The pH dependence and sequence composition effects are much less pronounced for MeP (and also P) containing oligonucleotides than for MeC containing ones. While oligonucleotide d(TTTMeCMeCMeCMeCTTTTMeCTTT) shows no longer any affinity to the target duplex above pH 6.5, oligonucleotide d(TTTMePMe...
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