Ballistic Brownian Motion of Nanoconfined DNA

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 singleelectron 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.

Activationless Electron Transfer of Redox-DNA in Electrochemical Nanogaps

“…As a result, chain motion cannot be the only factor kinetically controlling the current generation. Indeed, such fast DNA dynamics would theoretically generate currents in the hundreds of pA, whereas sub-pA-range currents were typically recorded in AFM-SECM for end-attached Fc-dT layers, Figure . , Besides, in the diffusive scenario, approach curves are predicted to display a pronounced 1/ d 2 signature (Figure S8), whereas the actual curves vary coarsely as 1/ d (inset in Figure ).…”

“…In order to assess the contributions of the DNA chain motion and of the electron transfer rate at the electrodes to the kinetic control of the tip current, we made use of the Q-Biol code, developed in our previous works. , Q-Biol is based on OxDNA, a nucleotide-level coarse-grained molecular dynamics model of DNA. It accurately reproduces the DNA chain motion and electron transfer events at the confining electrodes, Figure a …”

“…Using the term Nk tip ∞ as the sole adjustable parameter enabled a good agreement between the theoretical and experimental current approach curves to be obtained, down to d ∼ 3 nm, yielding a best-fit value of Nk tip ∞ = 4 cm/s (red trace in Figure ). Deviation from the fit for d < 3 nm can be attributed to the complex behavior of overconfined DNA chains (onset of ballistic motion, thermal effects), which was ignored here. Comparing the radius of the AFM-SECM tips (20−50 nm) to the interchain separation (∼8 nm), one can conclude that about N ∼ 10 chains may be contacted by the sharp tip, yielding k tip ∞ ∼ 0.4 cm/s.…”

“…The plateau current of the CVs corresponds to the saturation of the rate of electron transfer at high enough substrate and tip overpotentials, a feature uniquely predicted by the Marcus–Hush–Levich–Chidsey (MHLC) model of electron transfer kinetics. − The plateau current is thus given by where N is the number of Fc-DNA chains involved; e is the elementary charge; k tip ∞ and k sub ∞ are the heterogeneous electron transfer rate constants at infinitely large overpotentials at the tip and substrate, respectively; and ρ tip and ρ sub are the probabilities of the presence of the Fc head at the tip and substrate, respectively.…”

“…Such knowledge is now readily available through the molecular dynamics software Q-Biol, which we have been developing . Hence, the present work aims to systematically investigate, aided by Q-Biol, the electrochemical behavior of a diluted layer of Fc-terminated dT oligonucleotides (dT 50 ) end-anchored to a gold electrode, confined, and probed by an AFM-SECM tip.…”