Simulation data for 'Extraction and high-throughput sequencing of oak heartwood DNA - assessing the feasibility of genome-wide DNA methylation profiling'

Studies of the methylation state of DNA preserved in oak heartwood can help identify epigenetic tree ring features informing on past environmental conditions. Heartwood contains little DNA; large amounts of phenolic compounds are known to hinder the preparation of high-throughput sequencing libraries. To complement experiments, we simulated the interaction of double-stranded DNA (dsDNA) with a potential PCR inhibitor, the phenolic compound ellagic acid, by molecular dynamics and metadynamics techniques. Specifically, we investigated with molecular dynamics: (i) ellagic acid in water and in methanol; (ii) a model of dsDNA in water; (iii) multiple ellagic acids interacting with dsDNA in water and in methanol; (iv) dsDNA with an intercalated ellagic acid in water and in methanol. Moreover, with metadynamics, we explored the unbinding of an intercalated ellagic acid in dsDNA in water and in methanol.
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