DNA motion induced by electrokinetic flow near an Au coated nanopore surface as voltage controlled gate

Abstract

The diffusion and drift motion of λ DNA molecules on Au coated membrane surface near nanopores prior to their translocation through solid-state nanopores are investigated using fluorescence microscopy. With the capability of controlling electric potential at the Au surface as a gate voltage, Vgate, the motions of DNA molecules vary dramatically near the nanopores in our observations, presumably generated by electrokinetic flow. We carefully investigate theses DNA motions with different values of Vgate in order to alter the densities and polarities of counterions; which are expected to change the flow speed or direction, respectively. Depending on Vgate, our observations have revealed the critical distance from a nanopore for DNA molecules to be attracted or to be repelled, DNA’s anisotropic and unsteady drifting motions and accumulations of DNA molecules near the nanopore entrance. Further finite element method (FEM) numerical simulations indicate that the electrokinetic flow could explain these unusual DNA motions near metal collated gated nanopores qualitatively. Finally, we demonstrate the possibility to control the speed and direction of DNA motion near or through a nanopore, for example, recapturing a single DNA molecule multiple times with AC voltages on the Vgate.

Clog and Release, and Reverse Motions of DNA in a Nanopore

“…We observed and analyzed DNA dynamics near a nanopore and its direct translocation by fluorescence microscopy [7,29,30]. Through direct observation, we estimated the electric potential profile near a SiN nanopore [7].…”

“…Through direct observation, we estimated the electric potential profile near a SiN nanopore [7]. By applying a gate voltage to an Au film on a SiN nanopore membrane, anomalous DNA motions induced by electroosmotic flow via a pore were observed [29]. By using a field-effect transistor nanopore, we developed a method for slowing the translocation speed of DNA by applying pulse voltages only on the field-effect transistor gate electrode, while both ionic solutions in the trans and cis reservoirs were kept at V = 0 [30].…”

Gated Single-Molecule Transport in Double-Barreled Nanopores

“…It should be noted that this on/off behavior is reproducible with multiple cycles. Previous simulation studies by Sugimoto et al 52 suggested that the use of voltage gating to control DNA translocation is mainly influenced by (i) electrophoretic force under an applied V pore , (ii) electroosmotic flow, and (iii) electrostatic interactions between DNA and the nanopore surface. In this case, molecular transport across the nanopore is switched off when the gold electrode possesses a net negative charge ( V gate < −100 mV).…”

A Colloidal Nanopatterning and Downscaling of a Highly Periodic Au Nanoporous EGFET Biosensor

“…19,20 Not only that, in biomolecular detection, the potency of metallic nanopores includes an externally controllable electric potential owing to their ability to change flow direction by reversing the polarity of the potential difference between the pore and buffer solution. 21 Among expensive and complex nanostructuring and downscaling techniques including conventional lithography, electroplating, H3171 electron beam lithography (EBL) and the like, nanosphere lithography (NSL) has emanated as a simple and cheap colloid based lithography, particularly for the generation of highly periodic 2D metallic nanoparticles array on a large surface with 200-1000 nm range. 22,23 In this study, NSL was elaborated as the underlying process in Au nanoporous EGFET fabrication.…”