Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting

Rare and short-lived DNA conformations are proposed to be key drivers of mutagenesis, yet assessing their contribution to mutational signatures found in human cancers remains challenging. Here, we developed an approach that quantifies the sequence-dependent propensity to form a rare DNA conformation and compares the resulting fingerprint against cancer mutational signatures. Using ¹⁹ F NMR, we measured the propensity for the anionic Watson-Crick-like G•T ⁻ conformation across all sixteen triplet sequence contexts and discovered a striking 50-fold variation driven by suboptimal interactions between anionic thymine and its 3' neighbor. Comparing this fingerprint, and those of other rare DNA states, against the COSMIC database uncovered plausible links to mutational processes associated with exposure to damaging agents and therapies. Thus, integrating molecular biophysics with genomic epidemiology provides a powerful framework to explore how DNA’s dynamic properties shape genome stability and influence human disease.