Measuring DNA folding by the SARS-CoV-2 nucleocapsid protein.

Abstract

The SARS-CoV-2 virus is a deadly virus responsible for COVID-19. Here we are interested in the mechanics of how the nucleocapsid protein (N-protein) in SARS-CoV-2 folds the viral RNA into the capsid. This process could be a target for antiviral research which looks to prevent further proliferation of the virus. Our goal is to understand the role that electrostatic interactions play in the folding of the negatively charged RNA by the positively charged N-protein. To isolate these interactions from specific interactions with the RNA bases or conformation, we measure N-protein folding single molecules of double-stranded DNA. We take structural images of the folding using an atomic force microscope (AFM) or look at real-time folding using tethered particle motion (TPM) assays. We hypothesize that N-proteins might fold double-stranded DNA using a method similar to positively charged protamine proteins which act to package the DNA in sperm cells. These protamine proteins “bind and bend” the DNA in multiple locations using discrete, long-lived (∼100 s), reversible bending steps. We observe similar folding characteristics for N-protein, but also see some important differences. We will report on progress toward this goal.