Oligonucleotide probes containing pyrimidine analogs reveal diminished hydrogen bonding capacity of the DNA adduct O6-methyl-G in DNA duplexes

Abstract Oligonucleotide hybridization probes containing nucleoside analogs offer a potential strategy for binding specific DNA sequences that bear pro-mutagenic O 6 -G alkylation adducts. To optimize O 6 -Me-G-targeting probes, an understanding of how base pairs with O 6 -Me-G are stabilized is needed. In this study, we compared the ability of O 6 -Me-G and G to hydrogen bond with three pyrimidine-like nucleobases (Z, 4-thio-U, and 3-deaza-C) bearing varied hydrogen bond donor and acceptor groups. We found that duplexes containing the pyrimidine analog nucleoside:G pairs were more thermodynamically stable than those containing pyrimidine analog nucleoside: O 6 -alkyl-G pairs. Thus, hydrogen bonding alone was not sufficient to impart selectivity to probes that target O 6 -G alkylation adducts in DNA.