Oligodeoxynucleotides containing formamidopyrimidine lesions and C-nucleoside analogues at defined sites were prepared by solid-phase synthesis and in some cases enzymatic ligation. Formamidopyrimidine lesions were introduced as dinucleotides to prevent rearrangement to their pyranose isomers. Oligodeoxynucleotides containing single diastereomers of C-nucleoside analogues of Fapy·dA were introduced by using the respective phosphoramidites. The formamidopyrimidine lesions reduce the TM of dodecamers relative to their unmodified nucleotide counterparts when opposite the nucleotide proper base-pairing partner. However, duplexes containing Fapy·dG-dA mispairs melt significantly higher than those comprised of dG-dA. All duplexes containing Fapy·dA-dX or its C-nucleoside analogue melt lower than the respective complexes containing dA-dX. Studies of the alkaline lability of oligodeoxynucleotides containing formamidopyrimidine lesions indicate that Fapy·dA is readily identified as an alkali-labile lesion with use of piperidine (1.0 M, 90 °C, 20 min), but Fapy·dG is less easily identified in this manner.
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