Mechanical characterization of HIV-1 with a solid-state nanopore sensor

Abstract

Enveloped viruses fuse with cells to transfer their genetic materials and infect the host cell. Fusion requires deformation of both viral and cellular membranes. Since the rigidity of viral membrane is a key factor in their infectivity, studying the rigidity of viral particles is of great significance in understating viral infection. In this paper, a nanopore is used as a single molecule sensor to characterize the deformation of pseudo-type human immunodeficiency virus type 1 at sub-micron scale. Non-infective immature viruses were found to be more rigid than infective mature viruses. In addition, the effects of cholesterol and membrane proteins on the mechanical properties of mature viruses were investigated by chemically modifying the membranes. Furthermore, the deformability of single virus particles was analyzed through a recapturing technique, where the same virus was analyzed twice. The findings demonstrate the ability of nanopore resistive pulse sensing to characterize the deformation of a single virus as opposed to average ensemble measurements.

Keywords: Human immunodeficiency virus; Mechanical characterization; Resistive pulse; Solid-state nanopore; Viral maturity.

Figure 1.

(A) Schematic of virus translocation through nanopores. The color gradient shows the magnitude of electric field obtained from finite element simulation using COMSOL. The arrows show ionic flux through the nanopore. (B) Voltage-dependent electric field profiles near a nanopore without any particle calculated by the finite element simulation in COMSOL. (C) Representative current trace of virus sample and the negative control. Mature HIV-1 pseudostype virus was used.

Figure 2.

(A) TEM micrographs of all different virus samples. All scale bars are 100 nm. (B) Histograms of the virus diameter measured from the TEM micrographs. The black curves are Gaussian fittings. The total counts are written in white color. The insets show schematics of each viral structure. (C) Representative current traces for various virus samples. (D) Representatives of a single extracted resistive pulse event for each sample.

Figure 3.

(A) Bar graphs of relative peak amplitudes, the ratio of current drop amplitude (ΔI) divided by open-channel baseline current (I₀), for each sample at each applied voltage (B) Estimated effective aspect ratios of the viruses, calculated from finite element simulations.

Figure 4.

(A) Illustration of a recapture experiment (B) An example of current trace for recapturing showing both forward and reverse translocation events (C) The ratio of relative peak amplitudes in forward direction (1 V) to reverse direction (0.4 V) for the recapture events. The number on the bar represents the sample size of viruses for each category.