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Open AccessArticle

Clog and Release, and Reverse Motions of DNA in a Nanopore

Department of Mathematics and Physics, Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan
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Polymers 2019, 11(1), 84; https://doi.org/10.3390/polym11010084
Received: 24 November 2018 / Revised: 28 December 2018 / Accepted: 3 January 2019 / Published: 7 January 2019
(This article belongs to the Special Issue Polymer Translocation)
Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields near and inside the pores. We found significant clogging of nanopores by DNA molecules, particularly by circular DNA and linear T4 DNA (165.65 kbp). Here, the probabilities of DNA clogging events, depending on the DNA length and shape—linear or circular—were determined. Furthermore, two distinct DNA motions were observed: clog and release by linear T4 DNA, and a reverse direction motion at the pore entrance by circular DNA, after which both molecules moved away from the pore. Finite element method-based numerical simulations were performed. The results indicated that DNA molecules with pores 100–200 nm in diameter were strongly influenced by opposing hydrodynamic streaming flow, which was further enhanced by bulky DNA configurations. View Full-Text
Keywords: translocation; nanopore; DNA; electro-osmosis translocation; nanopore; DNA; electro-osmosis
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Kubota, T.; Lloyd, K.; Sakashita, N.; Minato, S.; Ishida, K.; Mitsui, T. Clog and Release, and Reverse Motions of DNA in a Nanopore. Polymers 2019, 11, 84.

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