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Radial dependence of DNA translocation velocity in a solid-state nanopore

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Microchimica Acta Aims and scope

Abstract

The physical features (such as size and charge) of a molecule transiting a nanopore whose cross-section area is only slightly larger than that of the molecule can be inferred from the measured ion-current through the pore. The transport of DNA molecules through nanopores has been extensively studied in the hope to enable low-cost and high-throughput DNA sequencing. However, the experimentally measured velocities of DNA translocation have a wide distribution, and this compromises the sequencing. In order to better understand the origin of the wide distribution, I have carried out molecular dynamics simulations to study the radial dependence of the translocation velocity. The results suggest a stick-slip type of motion of the dsDNA near the pore surface and a smooth translocation of the dsDNA near the pore center. The smooth dsDNA translocation (with a constant velocity) is governed by the zeta-potential of the pore surface which can be modified by adjusting the pH value and/or the ion concentration of the bulk electrolyte. This enables the mean translocation velocity of the dsDNA to be tuned and reduced. In addition, simulation results suggest that the smooth transport of dsDNA can be achieved by minimizing the dsDNA’s interaction with the pore, for example by chemical modification of its surface.

The smooth transport of DNA inside a solid-state nanopore can be achieved by repelling DNA away from the pore surface.

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Acknowledgments

The authors gratefully acknowledge useful discussion with Gustavo Stolovitzky and generous financial support from the IBM Bluegene Science Program.

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  1. IBM T J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA

    Binquan Luan

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  1. Binquan Luan
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Correspondence to Binquan Luan.

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Luan, B. Radial dependence of DNA translocation velocity in a solid-state nanopore. Microchim Acta 183, 995–1002 (2016). https://doi.org/10.1007/s00604-015-1589-2

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  • DOI: https://doi.org/10.1007/s00604-015-1589-2

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