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Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel.

ABSTRACT: We report experimental data on the unfolding of human and E. coli genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood diffusivity of confined DNA. The time scale emerging from our analysis has implications for genome mapping in nanochannels, especially as the technology moves towards longer DNA, by setting a lower bound for the delay time before making a measurement.

SUBMITTER: Reifenberger JG

PROVIDER: S-EPMC5823525 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel.

Reifenberger Jeffrey G JG Cao Han H Dorfman Kevin D KD

Macromolecules 20180124 3

We report experimental data on the unfolding of human and <i>E. coli</i> genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood dif ...[more]

PMID: 29479117

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