Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor

Abstract

Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1-nm-diameter pore exhibits sequence-specific hysteresis that arises from the reorientation of the DNA bases in the nanopore constriction. Such hysteresis of the DNA motion results in detectable changes of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand under an oscillating transmembrane bias. A strategy for sequencing DNA using electric-field pulses is suggested.High-throughput technology for sequencing DNA has already provided invaluable information about the organization of the human genome 1 and the common variations of the genome sequence among groups of individuals. 2 To date, however, the high cost of whole-genome sequencing limits widespread use of this method in basic research and personal medicine. Among the plethora of sequencing methods under development 3,4 that promise dramatic reduction of genome sequencing costs, the so-called nanopore methods 5,6 are among the most revolutionary. The main advantage of the nanopore method is that the sequence of nucleotides can be detected, in principle, directly from the DNA strand via electric recording, 7-18 requiring minimal reagents and having no limits on the length of the DNA fragment that can be read in one measurement.In this manuscript we investigate the feasibility of sequencing DNA using an alternating electric field in a nanopore capacitor. Through molecular dynamics (MD) simulations we demonstrate that back-and-forth motion of DNA in a 1-nm-diameter pore has a sequencespecific hysteresis that results in a detectable change of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand through the pore under an oscillating bias. Based on these observations, we propose a method for detecting DNA sequences by modulating the pattern of the applied alternating potential. We consider a single nanopore in a multilayered silicon membrane submerged in an electrolyte solution, Fig. 1. The capacitor membrane consists of two conducting layers (doped silicon) separated by a layer of insulator (silicon dioxide). An external electric bias V ex is applied across the membrane to drive a single DNA strand back and forth through the pore, while the electric potentials induced by the DNA motion are independently recorded at the top and bottom layers (electrodes) of the capacitor membrane, V top and V bot , respectively. Nanometer-diameter pores in such membranes have already been manufactured, 19-21 and the voltage signals resulting from the translocation of DNA strands through such pores have been recorded. 22 In particular, and is determined predominately by the electrolytic resistance, which is about 50-100 kΩ for KCl concentration in the 100 mM to 1 M range, and a parasitic capacitance associated with the membrane (<10 pF). The improvement in the bandwidth over patch clamping and prior measurements on hemolysin 7-10 and synthetic p...

Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores

“…22,23 Here we present a method that complements electrical measurements with high-sensitivity wide-field optical detection. Our method involves a customized total internal reflection fluorescence ͑TIRF͒ excitation, which permits low-background fluorescence probing on a nanometerthin SiN membrane immersed between two aqueous solutions.…”

Controlling molecular transport through nanopores

“…Another approach combined tunnelling electrodes with nanopores explored by several groups and holds the promise for DNA sequencing technology [104 -108]. The use of alternating electric fields might have some potential for analysis and control of the translocation process [109], but more work is needed to clarify the mechanism and feasibility. There are recent reports of controlling insertion of single-stranded DNA in carbon nanotubes [110]-which might open another avenue for the mass production of nanopores.…”

Solid-State Nanopore Sensors for Nucleic Acid Analysis

“…The appl presented g, [6] Astier, [7] C Gracheva, [16] Si Astier, [7] Clarke, [ , [30,31] Chen, [32] W lication of th d but are rev Clarke, [8] Cock igalov [17] opore DNA a Wanunu, [33] Wan hese new tec viewed in m kcroft, [9] Olasa nalysis. Metho r, [23] Olasagasti [ nunu [34] chniques to s ore detail by agasti, [10] [24] C sequencing y Branton.…”