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Slowing down DNA translocation through a nanopore by lowering fluid temperature

Authors


  • Colour Online: See the article online to view Figs. 1–7 in colour.

Correspondence: Professor Shizhi Qian, Institute of Micro/Nanotechnology, Old Dominion University, Norfolk, VA 23529, USA

E-mail: sqian@odu.edu

Fax: +1-757-683-3200

Abstract

In the next-generation nanopore-based DNA sequencing technique, the DNA nanoparticles are electrophoretically driven through a nanopore by an external electric field, and the ionic current through the nanopore is simultaneously altered and recorded during the DNA translocation process. The change in the ionic current through the nanopore as the DNA molecule passes through the nanopore represents a direct reading of the DNA sequence. Due to the large mismatch of the cross-sectional areas of the nanopore and the microfluidic reservoirs, the electric field inside the nanopore is significantly higher than that in the fluid reservoirs. This results in high-speed DNA translocation through the nanopore and consequently low read-out accuracy on the DNA sequences. Slowing down DNA translocation through the nanopore thus is one of the challenges in the nanopore-based DNA sequencing technique. Slowing down DNA translocation by lowering the fluid temperature is theoretically investigated for the first time using a continuum model, composed of the coupled Poisson–Nernst–Planck equations for the ionic mass transport and the Navier–Stokes equations for the hydrodynamic field. The results qualitatively agree with the existing experimental results. Lowering the fluid temperature from 25 to 0°C reduces the translocation speed by a magnitude of about 6.21 to 2.50 mm/sK (i.e. 49.82 to 49.71%) for the salt concentration at 200 and 2000 mM, respectively, improving the read-out accuracy considerably. As the fluid temperature decreases, the magnitude of the ionic current signal decreases (increases) when the salt concentration is high (sufficiently low).

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