Institute of Physics, Academia Sinica

Polymer Physics and Complex Fluids Group


Electrically-driven DNA Translocation through Biased Nanoelectrodes Embedded inside a Nanofluidic Channel

The new generation of high-speed, low-cost DNA sequencing technology has been proposed to be achieved by electrophoretically driving DNA through nanopores [1][2] or nanochannel [3][4], and then monitoring the change in the ionic current across the pore during the molecule's passage. When DNA translocates through the nanopore, the ionic current drops due to the blockage of nucleotide in the pore. This topic has drawn significant interest, but the device cannot directly observe the dynamics and structure of DNA as the nature of the required fundamental measurement forbids the use of fluorescent dyes, and relies mainly on inferring information from the ionic current signals.

To directly understand the dynamics of DNA when it translocates through the biased nanoelectrodes inside the nanofluidic channel, in simulation we first calculate the electric field inside the nanochannel, then use the pre-calculated electric field to perform Langevin dynamics simulation with coarse-grained DNA molecules (Fig. 1). For DNA in a folded structure, the translocation time is smaller than the unfolded case on average. The strength of longitudinal and transverse biased voltage also affects the drift velocity of DNA, which should match the speed resolution of the electronic measurements. This suggests an improvement for the design of the future applications of nanogaps in DNA sequencing.

[1] J.J Kasianowicz et al., PNAS, 1996, 93, 13770-13773 [2] D. Branton et al., Nat. Biotech., 2008, 26, 1146-1153 [3] X. Liang et al., Nano Lett., 2008, 8, 1472-1476 [4] M. Tsutsui et al., Sci. Rep., 2012, 2, 394