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Influence of Solution pH on DNA Translocation Velocity Through Alumina Nanopores

[+] Author Affiliations
Haojie Yang, Zaoqi Duan, Wei Si, Kun Li, Yunfei Chen

Southeast University, Nanjing, China

Paper No. IMECE2016-66403, pp. V010T13A040; 5 pages
doi:10.1115/IMECE2016-66403
From:
  • ASME 2016 International Mechanical Engineering Congress and Exposition
  • Volume 10: Micro- and Nano-Systems Engineering and Packaging
  • Phoenix, Arizona, USA, November 11–17, 2016
  • Conference Sponsors: ASME
  • ISBN: 978-0-7918-5064-0
  • Copyright © 2016 by ASME

abstract

Nanopores, which are promising as single-molecule sensing devices with low cost and high throughput, have offered significant insights into the research fields of static and dynamic molecular activities, properties, or interactions. In particular, due to its inherent sensitivity, high throughput, amplification-free sample preparation, nanopore will be potentially used in DNA sequencing. Nanopore-based sequencing is based on Coulter Counters, by measuring the distinct current reductions from individual DNA bases with different sizes as they are translocating through a nanopore. The sub-molecular details of an individual molecule can be gathered via recording modulations in the ionic current when a molecule passes through the nanopore under a bias voltage applied across the pore by two Ag/AgCl electrodes. The current blockage and dwell time obtained when the dsDNA translocates through nanopore are accumulated into scatter plots. Ionic current trace recorded at 1000 mv as 48kbp dsDNA translocate through 20 nm thickness with 35 nm alumina nanopore. Here, we apply Schrödinger’s first-passage-time distribution formula to study the distribution of DNA translocation time through alumina nanopores. The first-passage-time distribution is solved with the production of Fokker-Plank equation. Two useful parameters yielded the experimental results are analyzed: the diffusion constant of DNA inside the nanopore and the drift velocity of DNA translocation. By changing the pH value from 5.2 to 10.8 of the electrolyte solution, we notice that the drift velocity of DNA translocation and the diffusion constant of DNA inside the nanopore are extremely close to almost as 34 nm/μs. By changing the pH value of the electrolyte solution, we find that the surface charge density of the wall and the charge of the DNA molecule can be turned, which will result in different DNA molecule capture behaviors. The capture rate is about 17 s−1; the DNA molecule translocates through nanopore when the solution pH is 10.8; and 20 s−1 as the solution pH is 5.2. Theoretical modelling has also been conducted to analyze the experimental results. Hopefully, these findings will shed light on the transport properties of DNA in nanopores, which are relevant to future nanopore applications.

Copyright © 2016 by ASME
Topics: Nanopores , DNA

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