Resistive-Pulse DNA Detection with a Conical Nanopore Sensor

Abstract

In this paper, we describe resistive-pulse sensing of two large DNAs, a single-stranded phage DNA (7250 bases) and a double-stranded plasmid DNA (6600 base pairs), using a conically shaped nanopore in a track-etched polycarbonate membrane as the sensing element. The conically shaped nanopore had a small-diameter (tip) opening of 40 nm and a large-diameter (base) opening of 1.5 microm. The DNAs were detected using the resistive-pulse, sometimes called stochastic sensing, method. This entails applying a transmembrane potential difference and monitoring the resulting ion current flowing through the nanopore. The phage DNA was driven electrophoretically through the nanopore (from tip to base), and these translocation events were observed as transient blocks in the ion current. We found that the frequency of these current-block events scales linearly with the concentration of the DNA and with the magnitude of the applied transmembrane potential. Increasing the applied transmembrane potential also led to a decrease in the duration of the current-block events. We also analyzed current-block events for the double-stranded plasmid DNA. However, because this DNA is too large to enter the tip opening of the nanopore, it could not translocate the pore. As a result, much shorter duration current-block events were observed, which we postulate are associated with bumping of the double-stranded DNA against the tip opening.

Transport phenomena in nanofluidics

“…VI.F how synthetic cylindrical and conical nanopores can be fabricated. These pores have been used to investigate the translocation of DNA in folded and unfolded states Chen, Gu, Brandin, et al, 2004;Fologea, Gershow, Ledden, et al, 2005;Storm, Chen, Zandbergen, et al, 2005͒, the translocation duration of DNA ͑Heng et al, 2004;Mara et al, 2004;Karhanek et al, 2005;Harrell et al, 2006͒, which allows unraveling channel-molecule interactions with single-base-mismatch resolution ͑Iqbal et al, 2007͒, the blocked current amplitude during translocation of proteins ͑Han, Schurmann, , and nanobubbles, which dominate the noise ͑Smeets, Keyser, Wu, et al, 2006͒. Zhao et al ͑2007͒ revealed recently that the voltage threshold for permeation of double-stranded DNA bound to a restriction enzyme depends on the genetic sequence.…”

Detecting the translocation of DNA through a nanopore using graphene nanoribbons

“…Non-correlated events, characterized by fast and shallow dips in the ionic current, could be attributed to DNA molecules bumping against the pore instead of translocating through it 35 . During such bumping events, the clogging of the pore is too weak to effectively change the electrostatic potential in the proximities of the pore and gate the GNR.…”

Surface charge density of the track-etched nanopores in polyethylene terephthalate foils

“…Track-etched nanopores are fabricated by etching the ion tracks inside organic foils, 1 and they gain more and more attention due to their applications in biosensor, 2,3 DNA sequencing, 4,5 mimicking the ion channel, 6,7 and energy conversion. 8 In all these applications, surface charge is crucially important, since it governs ion transport through the pores, especially when the salt concentration is low.…”