Ballistic Brownian Motion of Nanoconfined DNA
Ignacio Madrid, Zhiyong Zheng, Cédric Gerbelot, Akira Fujiwara, Shuo Li, Simon Grall, Katsuhiko Nishiguchi, Soo Hyeon Kim, Arnaud Chovin, Christophe Demaille, Nicolas Clément
Abstract
Theoretical treatments of polymer dynamics in liquid generally start with the basic assumption that motion at the smallest scale is heavily overdamped; therefore, inertia can be neglected. We report on the Brownian motion of tethered DNA under nanoconfinement, which was analyzed by molecular dynamics simulation and nanoelectrochemistry-based single-electron shuttle experiments. Our results show a transition into the ballistic Brownian motion regime for short DNA in sub-5 nm gaps, with quality coefficients as high as 2 for double-stranded DNA, an effect mainly attributed to a drastic increase in stiffness. The possibility for DNA to enter the underdamped regime could have profound implications on our understanding of the energetics of biomolecular engines such as the replication machinery, which operates in nanocavities that are a few nanometers wide.