Synthesis of C8-arylamine-modified 2'-deoxyadenosine phosphoramidites and their site-specific incorporation into oligonucleotides

Abstract

Adducts of C8-(N-acetyl)-arylamines and 2’-deoxyadenosine were synthesised by palladium-catalysed C N cross-coupling chemistry. These 2’-dA adducts were converted into the corresponding 3’-phosphoramidites and site-specifically incorporated into DNA oligonucleotides, which were characterised by mass spectrometry, UV thermal-stability assays and circular dichroism. These modified oligonucleotides were also used in EcoRI restriction assays and in primer-extension studies with three different DNA polymerases. The incorporation of the 2’-dA lesion close to the EcoRI restriction site dramatically reduced the susceptibility of the DNA strand to cleavage; this indicates a significant local distortion of the DNA double helix. The incorporation of the acetylated C8-2’-dA-phosphoramidites into 20-mer oligonucleotides failed, however, because the Nacetyl group was lost during the deprotection process. Instead the corresponding C8-NH-2’-dA-modified oligonucleotides were obtained. The effect of the C8-NH-arylamine-dA lesion on the replication by DNA polymerases was clearly dependent both on the polymerase used and on the arylamine-dA damage.