Base Pairing and Replicative Processing of the Formamidopyrimidine-dG DNA Lesion

The 2,6-diamino-4-hydroxy-5-formamidopyrimidine of 2‘-deoxyguanosine (FaPydG) is one of the
major DNA lesions found after oxidative stress in cells. To clarify the base pairing and coding potential of
this major DNA lesion with the aim to estimate its mutagenic effect, we prepared oligonucleotides containing
a cyclopentane based analogue of the DNA lesion (cFaPydG). In addition, oligonucleotides containing the
cyclopentane analogue of 2‘-deoxyguanosine (cdG), and oligonucleotides containing 8-oxo-7,8-dihydro-2‘-deoxyguanosine (8-oxodG) were synthesized. The thermodynamic stability of duplexes containing these
building blocks and all canonical counterbases were determined by concentration dependent melting-point
measurements (van't Hoff plots). The data reveal that cFaPydG greatly destabilizes a DNA duplex (ΔΔG°298K
≈ 2−4 kcal mol-1). The optimal base pairing partner for the cFaPydG lesion is dC. Investigation of duplexes
containing dG and cdG shows that the effect of substituting the deoxyribose by a cyclopentane moiety is
marginal. The data also provide strong evidence that the FaPydG lesion is unable to form a base pair with
dA. Our computational studies indicate that the syn-conformation required for base pairing with dA is
energetically unfavorable. This is in contrast to 8-oxodG for which the syn-conformation represents the
energetic minimum. Kinetic primer extension studies using S. cerevisiae Pol η reveal that cFaPydG is
replicated in an error-free fashion. dC is inserted 2−3 orders of magnitude more efficiently than dT or dA,
showing that FaPydG is a lesion which retains the coding potential of dG. This is also in contrast to 8-oxodG,
for which base pairing with dC and dA was established.