Electrophoresis of Filamentous Viruses Through Solid State Nanopores

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Non-technical: This award by the Biomaterials program in the Division of Materials Research to Brown University is to study how filamentous viruses pass through extremely tiny pores. The pores are drilled through a thin layer of silicon nitride, which is a solid-state material and why they are referred to as solid-state nanopores. The viruses being used for this study belong to a class of bacterial phage and are isolated from infected E. coli. The viruses are skinny filaments of about one micrometer in length and only a few nanometers in diameter, and each one is identical in size because it consists of a single DNA chain coated by about three thousand copies of a small coat protein. Because the coat protein carries a few charges, the virus filament is charged along its length. When a solution containing the virus fills one side of a device containing a single nanopore, viruses can be driven through the nanopore, one by one, by applying a voltage across the device. When a virus passes through the nanopore, it blocks a characteristic amount of current for a brief but measurable duration. The goal of this project is to use the nanopore as a tool to study in microscopic detail how stiff charged molecules move through nanopores. This study essentially consists of comprehensive sets of measurements under carefully controlled conditions and with a number of different parameters. How the amount of current blocked and the speed of translocation change with parameters such as the amount of salt added to the solution, the size of the nanopore, and the voltage applied can tell us a great deal about the physical processes at play, all the way down to molecular scale. In spite of the conceptual simplicity of the study, the knowledge acquired can have profound technological implications. It may, for instance, lead to tiny devices for efficiently detecting and sorting various virus strains. The program will also provide multidisciplinary training of graduate and undergraduate students. The PIs and the graduate students have also planned, through the Brown Science Prep program, to deliver guest lectures, perform demonstrations, and host lab tours, all in order to broaden the impact of laboratory research on the surrounding area K-12 students and the general public. Technical: In this project, filamentous viruses will be used to study the fundamental physics of driven electrophoresis through nanoscale pores. The physical properties of filamentous viruses, including their charge density, their stiffness, and their length, are both precisely known and easily tunable. That control enables us to systematically test theoretical models of electrophoresis inside a nanopore at the single-molecule level. The planned study includes measurements of the capture process, the amount of current blocked, the translocation speed, and the spread of individual translocation times. With this study, the effects of filament stiffness on translocation speed under a range of driving voltages will be studied. In addition, factors that account for the dispersion in translocation speed will also be determined. The experimental results will be compared with theoretical calculations based on the coupled Navier-Stokes and Poisson Boltzmann equations, and also compared with computer simulations driven by Langevin dynamics. By addressing every facet of nanopore translocations, including the capture process, the electrokinetic pulling force, and the viscous drag that opposes it, the planned experiments will provide quantitative tests of the established theoretical models. Thus, students working on the program will acquire comprehensive training in the cutting-edge, nano-technology field. The planned outreach efforts, coordinated by the Brown Science Prep program, focus on connecting physics knowledge with device technology, via guest lectures, lab tours, and demos both live and through online videos.