Synthesis and Characterization of Oligodeoxynucleotides Containing Formamidopyrimidine Lesions and Nonhydrolyzable Analogues

Abstract

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 T_M 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.