Monitoring the Escape of DNA from a Nanopore Using an Alternating Current Signal

Abstract

We present the use of an alternating current (AC) signal as a means to monitor the conductance of an α-hemolysin (αHL) pore as a DNA hairpin with a polydeoxyadenosine tail is driven into and released from the pore. Specifically, a 12 base pair DNA hairpin attached to a 50-nucleotide poly-A tail (HP-A 50 ) is threaded into an αHL channel using a DC driving voltage. Once the HP-A 50 molecule is trapped within the αHL channel, the DC driving voltage is turned off and the conductance of the channel is monitored using an AC voltage. The escape time, defined as the time it takes the HP-A 50 molecule to transport out of the αHL channel, is then measured. This escape time has been monitored as a function of AC amplitude (20 to 250 mV ac ), AC frequency (60-200 kHz), DC drive voltage (0 to 100 mV dc ), and temperature (−10 to 20 °C), in order to determine their effect on the predominantly diffusive motion of the DNA through the nanopore. The applied AC voltage used to monitor the conductance of the nanopore has been found to play a significant role in the DNA/nanopore interaction. The experimental results are described by a onedimensional asymmetric periodic potential model that includes the influence of the AC voltage. An activation enthalpy barrier of 1.74 × 10 −19 J and a periodic potential asymmetry parameter of 0.575 are obtained for the diffusion at zero electrical bias of a single nucleotide through αHL.

Disentangling Steric and Electrostatic Factors in Nanoscale Transport Through Confined Space

“…Similarly, the inclusion of porebiopolymer interactions into an expanded model can benefit from previous work in this area. 64,69 We note that our results on the charge-induced slowing down of DNA strands may also be applicable to several nanopore-based DNA strand sequencing techniques in which it is often difficult to achieve high signal-to-noise ratios for speedily translocating DNA strands. Our concept of partial charge neutralization for delayed DNA translocation could furthermore be extended to nucleic acid derivatives that carry a different partially neutral DNA backbone as well as the detection of DNA mutations.…”

“…An expression for the hopping rates is given by ݇ ା ൌ ݇ሺ݉ሻ * ݁ ିఈ * ሺ ାଵሻ ݇ ି ൌ ݇ሺ݉ሻ * ݁ ሺଵିఈሻ * ሺ ାଵሻ (6) and depends on ∆(m) that gives the difference in energy between two consecutive states and is defined by 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 translocating αHL in the 5′ to 3′ direction. 64 Using the hopping rates, the total theoretical translocation times <t> can be calculated using…”

Direct numerical simulation of electrokinetic translocation of a cylindrical particle through a nanopore using a Poisson–Boltzmann approach

“…One of the most important nanopore-based sensing techniques originated from the Coulter counter [18], in which the particle counting is on the basis of the change in the ionic current arising from the particle translocation through an aperture. Benefit from the advent in the state-of-the-art nanofabrication technologies, artificial nanopores has been successfully fabricated [19][20][21][22], which enables the nanopore-based sensing at one single molecule level for various bio-analytical applications [23][24][25][26]. Numerous studies have been performed to investigate the electrokinetic particle translocation through a nanopore and the corresponding ionic current response [19][20][21][22].…”

Translocation dynamics of a short polymer driven by an oscillating force

“…This has provided new insights into the DNA conformations. [13][14][15][16][17][18][19] Moreover, the living cells give rise to a fluctuating environment. As a consequence, the polymers are subject to time dependent driving forces, which drive the biological system far away from equilibrium.…”

“…As a consequence, the polymers are subject to time dependent driving forces, which drive the biological system far away from equilibrium. 18,19 Several different theoretical models try to predict the complex translocation features. This, under different conditions of geometrical confinements of the molecule, pore interaction, inertia and/or different time dependent driving mechanisms.…”