DNA capture into the ClyA nanopore: diffusion-limited versus reaction-limited processes

Abstract

The capture and translocation of biomolecules through nanometer-scale pores are processes with a potentially large number of applications, and hence they have been intensively studied in recent years. The aim of this paper is to review existing models of the capture process by a nanopore, together with some recent experimental data of short single- and double-stranded DNA captured by the Cytolysin A (ClyA) nanopore. ClyA is a transmembrane protein of bacterial origin which has been recently engineered through site-specific mutations, to allow the translocation of double- and single-stranded DNA. A comparison between theoretical estimations and experiments suggests that for both cases the capture is a reaction-limited process. This is corroborated by the observed salt dependence of the capture rate, which we find to be in quantitative agreement with the theoretical predictions.

Voltage-driven translocation: Defining a capture radius

“…The field outside the pore is often modeled using the point-like approximation 15,27,28 , which greatly simplifies analytical calculations; for a pore of radius r p and length l, the corresponding potential V (r) is the second equation in the Introduction. The part of the total potential gradient ∆V that is relevant for capture depends on the ratio of the access (ac) and channel (ch) resistances.…”

“…is the point-charge approximation 15,[27][28][29] for the electric potential at a distance r when a voltage difference ∆V is applied across the system. Here r e = r p /( 2l rp + π) is the characteristic length of the electrostatic potential outside a pore of radius r p and length l 28 . The capture radius is then defined as the distance R * at which W (R * ) = k B T 15,27,29 .…”

“…Alternatively, we can define the capture radius as the point of no return 15,25,28 (or event horizon to borrow an expression from General Relativity), i.e. the distance below which the particle cannot escape the attraction of the pore.…”

Influence of Electrolyte Concentration on Single-Molecule Sensing of Perfluorocarboxylic Acids

“…It was worth noting that the increase of blockade from 3 to 4 M KCl (1.99%) was actually smaller than the value from 2 to 3 M KCl (2.84%), which was partially in agreement with the greater slope of the voltage induced decrease of ∆I/I 0 in 2 M KCl. One possible explanation for such phenomena was the reduced Debye length at an elevated concentration of electrolyte ( Nomidis et al, 2018 ). As the salt concentration increased, the contribution of counterion screening was inhibited, and the current blockade became more determined by the steric exclusion effect ( Wilson et al, 2019 ), or in other words, reflecting mainly the structural properties of PFCAs.…”

Electrode-free nanopore sensing by DiffusiOptoPhysiology

“…Although numerous efforts have been made to counteract the electrophoretic force during DNA translocation ( 46 ), the electrophoretic force, which efficiently untangles coiled DNA during translocation ( 47 ), was still considered indispensable during DNA sensing. However, the long persistence length of dsDNA ( 48 ) and the wide opening of ClyA nanopore may reduce the entropic barrier for dsDNA translocation ( 49 ). Furthermore, the relatively large vestibule of ClyA may also serve to accommodate dsDNA in a form of partial translocation to report the sensing signal of dsDNA during the DOP recording as well.…”