ArticleThe journal of physical chemistry letters2026
Influence of DNA Mispairing and Abasic Sites on Duplex Dynamics: A Temperature-Jump Infrared Spectroscopy Study.
Article in The journal of physical chemistry letters, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
The dynamics of double-stranded DNA (dsDNA) are central to its biological role as a repository of genetic information. However, under physiological conditions DNA is subject to base mispairing and the formation of abasic sites through processes such as depurination. Such site-specific changes to the established Watson-Crick (WC) architecture would be expected to influence duplex dynamics and so affect key processes including protein binding. Here, we apply temperature-jump infrared spectroscopy to interrogate the relative impact of base pair mismatches and abasic sites on the structural dynamics of a 21-base pair (bp) dsDNA oligomer. The inclusion of an abasic site in the center of the strand leads to destabilization that is manifest as <1 μs time scale disruption of the nearby bases that is not present in fully WC-base paired sequences. Comparing this behavior with sequences featuring mismatches of different sizes shows that a single-bp mismatch causes minimal destabilization, whereas a triple base mismatch results in dynamics that closely mimic those resulting from the presence of an abasic site.
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