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

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...

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Bibliographic Details
Published in:Biomicrofluidics 2019-07, Vol.13 (4), p.044110-044110
Main Authors: Bhandari, Aditya Bikram, Dorfman, Kevin D.
Format: Article
Language:English
Subjects:
Asymptotic methods
Asymptotic properties
Computer simulation
Deoxyribonucleic acid
DNA
Genomes
Mapping
Nanochannels
Regular
Simulation
Skewed distributions
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Summary: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.
ISSN:1932-1058
1932-1058
DOI:10.1063/1.5109566