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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 dsDNA, 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 of a few nanometers wide.
Supplementary materials
Title
Ballistic Brownian motion of nanoconfined DNA
Description
Supplementary Figures; Supplementary Table; Supplementary Discussion of Dissecting the power spectral density of the z position, Sz obtained from MD for dT20 and (dT.dA)20 and peak splitting, analysis of <τup>, <τdown>, MD analysis for 35-mer DNA, interpretation of CV and AFM-SECM results, interpretation of k0, ρH2 and kV, additional experiments with dT35 and (dT.dA)35; Supporting references.
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