Chemical Biology of N⁵-Substituted Formamidopyrimidine DNA Adducts

DNA nucleobases are the prime targets for chemical modifications by endogenous and exogenous electrophiles. Alkylation of the N7 position of guanine and adenine in DNA triggers base-catalyzed imidazole ring opening and the formation of N⁵-substituted formamidopyrimidine (N⁵-R-FAPy) lesions. Me-FAPy-dG adducts induced by exposure to methylating agents and AFB-FAPy-dG lesions formed by aflatoxin B₁ have been shown to persist in cells and to contribute to toxicity and mutagenicity. In contrast, the biological outcomes of other N⁵-substituted FAPy lesions have not been fully elucidated. To enable their structural and biological evaluation, N⁵-R-FAPy adducts must be site-specifically incorporated into synthetic DNA strands using phosphoramidite building blocks, which can be complicated by their unusual structural complexity. N⁵-R-FAPy exist as a mixture of rotamers and can undergo isomerization between α, β anomers and furanose-pyranose forms. In this Perspective, we will discuss the main types of N⁵-R-FAPy adducts and summarize the strategies for their synthesis and structural elucidation. We will also summarize the chemical biology studies conducted with N⁵-R-FAPy-containing DNA to elucidate their effects on DNA replication and to identify the mechanisms of N⁵-R-FAPy repair.