Toward De Novo Recapitulation of Cytoskeleton Dynamics with DNA Nanotubes

Abstract

The polymerization and depolymerization of cytoskeleton can transduce chemical energy into mechanical energy that drives cellular motility, such as chromosome segregation to cell protrusion. De novo recapitulation of the cytoskeletal phenomena with synthetic material would test our understanding of the design principles of polymerization motors. In the DNA nanotechnology tool box, DNA nanotubes are arguably the closest counterparts of cytoskeleton and we aim to utilize such structures to synthesize artificial cytoskeletons with various levels of complexity. DNA nanotube polymerization was monitored using total internal reflection microscopy at the single molecule level. We observed that DNA nanotubes exhibit asymmetric polymerization, similar to actin and microtubule polymerizations. We measured the association and dissociation rates of DNA nanotube polymerization at different monomer concentrations and temperatures and compared our measurements with the polymerization theory developed for the cytoskeleton and the kinetic DNA tile assembly model. Finally, the coupling between DNA nanotube polymerization and a DNA nanotechnology analog of nucleotide hydrolysis could potentially recapitulate cytoskeleton-based dynamics, such as treadmilling and dynamic instability, where the polymerization and depolymerization co-exist at steady state without ever reaching equilibrium.