Oligodeoxynucleotides containing formamidopyrimidine lesions and C-nucleoside analogues at defined sites were prepared by solid-phase synthesis and in soma oases enzymatic ligation. Formamidopyrimidine lesions were introduced as dinucleotides to prevent rearrangement to their pyranose isomers. Oligodeoxynucleotides containing single diastereomers of C-nucleoside analogues of Fady(.)dA were introduced by using the respective phosphoramidites. The formamidopyrimidine lesions reduce the T 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 degreesC, 20 min), but Fapy(.)dG is less easily identified in this manner.