Simulations corroborate telegraph model predictions for the extension distributions of nanochannel confined DNA

Aditya Bikram Bhandari, Kevin D. Dorfman

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Abstract

Hairpins in the conformation of DNA confined in nanochannels close to their persistence length cause the distribution of their fractional extensions to be heavily left skewed. A recent theory rationalizes these skewed distributions using a correlated telegraph process, which can be solved exactly in the asymptotic limit of small but frequent hairpin formation. Pruned-enriched Rosenbluth method simulations of the fractional extension distribution for a channel-confined wormlike chain confirm the predictions of the telegraph model. Remarkably, the asymptotic result of the telegraph model remains robust well outside the asymptotic limit. As a result, the approximations in the theory required to map it to the polymer model and solve it in the asymptotic limit are not the source of discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA during genome mapping. The agreement between theory and simulations motivates future work to determine the source of the remaining discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA in nanochannels used for genome mapping.

Original languageEnglish (US)
Article number044110
JournalBiomicrofluidics
Volume13
Issue number4
DOIs
StatePublished - Jul 1 2019

Bibliographical note

Funding Information:
We thank Bernhard Mehlig and Daniel Ödman for discussions about their theoretical distributions and Guo Kang Cheong for discussions about PERM simulations. This work was supported by the National Institutes of Health (NIH) (No. R01-HG006851). Computational resources were provided in part by the Minnesota Supercomputing Institute.

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