Nanopore Measurements of Filamentous Viruses Reveal a Sub-nanometer-Scale Stagnant Fluid Layer

Abstract

We report measurements and analyses of nanopore translocations by fd and M13, two related strains of filamentous virus that are identical except for their charge densities. The standard continuum theory of electrokinetics greatly overestimates the translocation speed and the conductance associated with counterions for both viruses. Furthermore, fd and M13 behave differently from one another, even translocating in opposite directions under certain conditions. This cannot be explained by Manning-condensed counterions or a number of other proposed models. Instead, we argue that these anomalous findings are consequences of the breakdown of the validity of continuum hydrodynamics at the scale of a few molecular layers. Next to a polyelectrolyte, there exists an extra-viscous, sub-nanometer-thin boundary layer that has a giant influence on the transport characteristics. We show that a stagnant boundary layer captures the essential hydrodynamics and extends the validity of the electrokinetic theory beyond the continuum limit. A stagnant layer with a thickness of about half a nanometer consistently improves predictions of the ionic current change induced by virus translocations and of the translocation velocity for both fd and M13 over a wide range of nanopore dimensions and salt concentrations.

Osmotically Driven and Detected DNA Translocations

“…But Eq. 5 does not account for the viscous drag forces that act on the parts of the polymer outside the nanopore that the nanopore reels in from large distances 36 , nor does it account for known shortcomings of the nonlinear Poisson-Boltzmann equation 20 . In the case of voltage-driven translocations, those effects suppress v by a factor of 14 relative to the analogous theoretical prediction by Ghosal 37,38 .…”

“…The analysis of ionic current recordings was performed in two stages using custom MATLAB programs similar to those described in refs 20,26,39,40 . First, a program identified the approximate locations of all significant blockage events in the current recordings.…”

“…2 by the grey and black points in the scatter plots. To determine the translocation drift speed for each condition, we fit a first passage time function to the distribution of the duration of only unfolded translocations 20 .…”

“…assumed that the nanopore surface is neutral, that its interaction with the solute is repulsive, and that there is a nonzero slip length in the fluid flow profile 19 . Those assumptions are at odds with the fact that the charge densities on the surfaces of silicon nitride nanopores can be highly negative, hence they attract counterions 20 , and that it is necessary for the nanopore to be hydrophillic to measure DNA translocations. The model of Hatlo et al .…”

Accurate modeling of a biological nanopore with an extended continuum framework

“…However, in small nanopores (≤ 10 nm radius), they comprise a significant fraction of the total nanopore radius and hence must be taken into account. 54,58,63,81 In continuum simulations, this can be achieved with the use pf positional-dependent ion diffusion coefficients. An example implementation is the 'soft-repulsion PNP' developed by Simakov and Kurnikova, 63,70 who used it to predict the ionic conductance of the αhemolysin nanopore.…”