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 develop an approach that quantifies the sequence-dependent propensity to form a rare DNA conformation and compare the resulting fingerprint against cancer mutational signatures. Using 19F NMR, we measure the propensity for the anionic Watson-Crick-like G•T- conformation across all sixteen triplet sequence contexts and discover 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 Catalogue of Somatic Mutations in Cancer (COSMIC) database uncovers 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.