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Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity

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Abstract

Here we present a pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution. Using a principle familiar from classic devices based on soft-lithography, the system uses pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit. We use this system to quantify the interactions of multiple confined DNA chains, a key problem in polymer physics with important implications for nanofluidic device performance and DNA partitioning/organization in bacteria and the eukaryotes. In particular, we focus on the problem of two-chain confinement, using differential staining of the chains to independently assess the chain conformation, determine the degree of partitioning/mixing in the cavities and assess coupled diffusion of the chain center-of-mass positions. We find that confinement of more than one chain in the cavity can have a drastic impact on the polymer dynamics and conformation.

Graphical abstract: Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity

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Publication details

The article was received on 13 Jul 2018, accepted on 28 Aug 2018 and first published on 06 Sep 2018


Article type: Paper
DOI: 10.1039/C8SM01444B
Citation: Soft Matter, 2018, Advance Article
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    Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity

    X. Capaldi, Z. Liu, Y. Zhang, L. Zeng, R. Reyes-Lamothe and W. Reisner, Soft Matter, 2018, Advance Article , DOI: 10.1039/C8SM01444B

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