Nanopore tomography for quantitative assessment of geometrical parameters of filamentous fd bacteriophage

An understanding of the morphology of viruses is critical to understanding their function in a physiological environment as well as for modern, bio-inspired applications. Several imaging techniques including TEM and AFM have been used to characterize single particles. However, there is a need for a rapid and high-throughput method. Nanopore tomography (NT) is an emerging single-particle technique with the ability to measure the geometrical features of individual viruses.

In this work, we apply NT methodology to measure the diameter of fd, a long, filamentous bacteriophage translocating through a solid-state nanopore at high salt concentrations. The diameter of the virus is subject to inference from experimentally reported changes in current. Continuum simulations are performed to estimate the phage diameter from these current blockades. Furthermore, the robustness and sensitivity of these estimates to variations in the physicochemical and geometrical parameters of the system are investigated. In addition, we present and benchmark helium ion microscopy (HIM) as an alternative imaging technique superior to widely used TEM and AFM.

The calculated diameters match closely with the measurements using standard imaging techniques. The methodology is high throughput, requires minimal sample preparation, and performs favorably as compared to the other standard imaging techniques. In conclusion, this study serves as a proof-of-concept for the use of NT to characterize small viruses.