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What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences

Yonetani, Yoshiteru; Kono, Hidetoshi

The lifetime during which a water molecule resides at the surface of a biomolecule varies according to the hydration site. What determines this variety of lifetimes? Despite many previous studies, there is still no uniform picture quantitatively explaining this phenomenon. Here we calculate the lifetime for a particular hydration pattern in the DNA minor groove, the water bridge, for various DNA sequences to show that the water-bridge lifetime varies from 1 to 300 ps in a sequence-dependent manner. We find that it follows 1/k ($$V$$$$_{step}$$)$$P$$$$_{m}$$, where $$P$$$$_{m}$$ and $$V$$$$_{step}$$ are two crucial factors, namely the probability of forming a specific hydrogen bond in which more than one donor atom participates, and the structural fluctuation of DNA, respectively. This relationship provides a picture of the water kinetics with atomistic detail and shows that water dissociation occurs when a particular hydrogen-bonding pattern appears.



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Category:Biochemistry & Molecular Biology



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