Impact of thymine glycol damage on DNA duplex energetics: Correlations with lesion-induced biochemical and structural consequences

ABSTRACT The magnitude and nature of lesion‐induced energetic perturbations empirically correlate with mutagenicity/cytotoxicity profiles and can be predictive of lesion outcomes during polymerase‐mediated replication in vitro. In this study, we assess the sequence and counterbase‐dependent energetic impact of the Thymine glycol (Tg) lesion on a family of deoxyoligonucleotide duplexes. Tg damage arises from thymine and methyl‐cytosine exposure to oxidizing agents or radiation‐generated free‐radicals. The Tg lesion blocks polymerase‐mediated DNA replication in vitro and the unrepaired site elicits cytotoxic lethal consequences in vivo. Our combined calorimetric and spectroscopic characterization correlates Tg‐induced energetic perturbations with biological and structural properties. Specifically, we incorporate a 5R‐Tg isomer centered within the tridecanucleotide sequence 5′‐GCGTACXCATGCG‐3′ (X = Tg or T) which is hybridized with the corresponding complementary sequence 5′‐CGCATGNGTACGC‐3′ (N = A, G, T, C) to generate families of Tg‐damaged (Tg·N) and lesion‐free (T·N) duplexes. We demonstrate that the magnitude and nature of the Tg destabilizing impact is dependent on counterbase identity (i.e., A ∼ G