Physical Virology with Atomic Force and Fluorescence Microscopies: Seeing and Touching Viruses and Protein Cages

Viruses can be described as nanocontainers that transport their nucleic acids until reaching a convenient host for genome delivery. These molecular machines hijack the host's cellular machinery to ensure their own progeny. Along the viral life cycle, virus particles implement tasks, such as self-assembly, packaging and protection of nucleic acids, host cell recognition, and genome release. Therefore, virus particles need to be stable enough to protect their genome yet simultaneously be prepared to release their cargo during uncoating when triggered by the appropriate physicochemical cues. In this vein, AFM has been revealed as a powerful technique to gain insights into virus structure and function. Beyond imaging virus particles in liquid milieu, AFM also allows their manipulation at the nanoscale and the exploration of every material property that can be evaluated by measuring the mechanical perturbation of the cantilever. In this chapter, we start by revising some recipes for adsorbing protein shells on surfaces. Then we describe AFM approaches to study individual virus particles, ranging from imaging to manipulation methodologies for studying virus biomechanics and inducing virus disassembly. We also explain how a convenient combination of AFM and fluorescence methodologies helps in studying the function of virus-based nanoparticles.