Dynamics and Conformation of Electrically-Driven DNA Translocation through Biased Nanoelectrodes Embedded inside a Nanofluidic Channel
Guo-Jun Liao1*, Leonardo Lesser-Rojas2, Kevin Shen1, Chia-Fu Chou1,3,4, Yeng-Long Chen1,5
1Institute of Physics, Academia Sinica, Taipei, Taiwan
2CICANUM, School of Physics, University of Costa Rica, San José, Costa Rica
3Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
4Genomics Research Center, Academia Sinica, Taipei, Taiwan
5Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
* presenting author:Guo-Jun Liao, email:gjliao@gate.sinica.edu.tw
Novel high-speed, low-cost DNA sequencing technology has been proposed to be achieved by electrophoretically driving DNA through nanopores and monitoring the change in the ionic current across the pore during the molecule’s passage [1-2]. Electrode-embedded nanopore has been demonstrated theoretically to differentiate nucleotides by different levels of current change [3]. The current challenges to be overcome are the fast time resolution of the electronic measurements for each nucleotide passage and the signal-to-noise related issues arising from the DNA conformational fluctuations in nanopore. It is proposed that these issues may be solved in nanofluidics flow with externally applied transverse electric potential bias to slow the translocation process and reduce conformational fluctuations [4-5].

We investigated the effect of longitudinal and transverse biased voltage on the DNA translocation process. We directly model the dynamics of DNA as it translocates through the biased nanoelectrodes inside the nanofluidic channel. In our simulation, we first calculate the electric field inside the nanochannel, and use the pre-calculated electric field to perform Langevin dynamics simulation with coarse-grained DNA molecules. We found that the strength of the longitudinal electrical field is inversely proportional to the translocation time. The relationship between DNA structure and translocation time is found to be consistent with the experimental results in literature. Our findings suggest an improvement for the design of the future applications of nanogaps for DNA sequencing.

References
1. J.J Kasianowicz et al., PNAS, 93, 13770-13773 (1996)
2. D. Branton et al., Nat. Biotech., 26, 1146-1153 (2008)
3. J. Langerqvist et al., Nano Lett., 6, 779-782 (2006)
4. X. Liang et al., Nano Lett., 8, 1472-1476 (2008)
5. L. Lesser-Rojas, et al. Biomicrofluidics 8, 016501 (2014)


Keywords: DNA translocation, Langevin dynamics simulation, nano-fluidics