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• W2003879304 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(TTTMePMePMePMePTTTTMePTTT) displays preserved binding with a Tm of 32.5 °C at pH 7.0 and even binds with a Tm of 23.3 °C at pH 8.0. Oligonucleotides containing POMe show distinctly less stable triple helices. The average decrease in Tm/modification for oligonucleotide d(TTTTTPOMeTPOMeTPOMeTPOMeTPOMeT) at pH 6.5 is 6.7 °C relative to the MeC containing oligonucleotide. DNase I footprint titration experiments indicate that d(TTTTTMePTMePTMePTMePTMePT) binds not only five times stronger to a 229 base pair DNA fragment than d(TTTTTMeCTMeCTMeCTMeCTMeCT) but also with higher selectivity. UV-melting experiments show that duplexes of d(TTTTTCTXTCTCTCT) (where X = P, MeP, or POMe) with their antiparallel Watson−Crick complement are dramatically less stable (ΔTm < −12 °C) at pH 8.0 than the corresponding natural duplex. Thus the new bases P and MeP show Hoogsteen specific pairing behavior." @default.
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• W2003879304 date "1997-06-01" @default.
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• W2003879304 title "5-Substituted 2-Aminopyridine <i>C</i>-Nucleosides as Protonated Cytidine Equivalents: Increasing Efficiency and Selectivity in DNA Triple-Helix Formation" @default.
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• W2003879304 doi "https://doi.org/10.1021/ja9704904" @default.
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