DNA Electrokinetic Translocation through a Nanopore: Local Permittivity Environment Effect

Abstract

The effect of the local liquid permittivity surrounding the DNA nanoparticle, referred to as the local permittivity environment (LPE) effect, on its electrokinetic translocation through a nanopore is investigated for the first time using a continuum-based model, composed of the coupled Poisson−Nernst−Planck (PNP) equations for the ionic mass transport and the Stokes and Brinkman equations for the hydrodynamic fields in the region outside of the DNA and within the ion-penetrable layer of the DNA nanoparticle, respectively. The nanoparticle translocation velocity and the resulting current deviation are systematically investigated for both uniform and spatially varying permittivities surrounding the DNA nanoparticle under various conditions. The LPE effect in general reduces the particle translocation velocity. The LPE effect on the current deviation is insignificant when the imposed electric field is relatively high. However, when the electric field and the bulk electrolyte concentration are relatively low, both current blockade and enhancement are predicted with the LPE effect incorporated, while only current blockade is predicted with the assumption of constant liquid permittivity. It is thereby shown that regardless of the electric field imposed the predictions on ionic current with considering the LPE effect are in good qualitative agreement with the experimental observations obtained in the literature.

Slowing down DNA translocation through a nanopore by lowering fluid temperature

“…Typically, the total number of the mesh is approximately 160 000. The numerical model has been verified in the previous studies on the distributions of ions and electric potential near a charged planar surface and EOF in a cylindrical nanopore as well as on the electrophoretic motion of a rigid/soft nanoparticle in a nanopore . All results presented below are ensured to be convergent and mesh‐independent through stringent tests.…”

“…The latter corresponds to a dsDNA with ca. 14 helical pitches . Here, L p is a little shorter than the persistence length of dsDNA (ca.…”

“…Since the size of fluid reservoirs is usually much larger than that of the nanopore, the local electric field within the nanopore is significantly higher than that in the fluid reservoir, resulting in slow particle motion within the fluid reservoir and high translocation velocity inside the nanopore. One of the major challenges in the nanopore‐based technique is that DNA nanoparticles translocate through the nanopore too fast to be accurately detected . Although one can reduce the voltage bias applied across the nanopore to reduce the electric field inside the nanopore and consequently slow down the DNA translocation, lower voltage bias will simultaneously reduce the capture rate of the nanopore and the magnitude of the current change, leading to lower throughput and read‐out accuracy.…”

“…Therefore, a relatively high voltage bias is typically applied across the nanopore in the nanopore‐based DNA sequencing applications. To now, several methods have been proposed to slow down the DNA translocation through the nanopore to achieve higher read‐out accuracy . They include increasing the solvent viscosity to increase the viscous drag force on the particle, lowering the fluid temperature to increase the fluid viscosity, adjusting salt concentration and/or salt type to modify the charge property of the nanopore by chemical functionalization of the nanopore or by an ionic field effect transistor, imposing a salt concentration gradient, utilizing optical tweezers, and conducting nanopores .…”

Reluctance of a neutral nanoparticle to enter a charged pore

“…It, however, turns out that the numerical treatment of the fully three-dimensional problem is still very demanding, even on modern computers, if a satisfactory numerical accuracy is required. Consequently, similar previous studies are restricted to onedimensional [35], two-dimensional [25], or axisymmetric problems [24,[39][40][41][42] problems. In the latter case, which is also at the focus of our present work, an effectively two-dimensional problem is readily recovered when going over to cylindrical coordinates (see e.g.…”