Electrode-Tethered DNA: Interfacial Mechanics and Switching Dynamics from Ensemble-Level Atomistic Simulations

Surface-tethered DNA, anchored to gold by the late 1990s, has matured into a versatile platform for biosensing, computing and actuation. Whereas the molecular behavior of DNA in bulk solution is well characterized, that of DNA at electrode interfaces remains far less understood. Here we investigate the mechanics and dynamics of electrode-tethered double-stranded DNA across surface chemistries, salt concentrations and applied potentials. Using GPU-accelerated all-atom molecular dynamics, we sample trajectory ensembles totaling 144 s over 620 simulations. The simulations reproduce key experimental observations yet uncover molecular behavior that had gone unnoticed despite nearly three decades of research. Ensemble statistics reveal a preferred orientation about the helical axis upon surface contact. Energetic analysis identifies a substantial role for Onsager-Samaras-type repulsion in opposing that contact. By reproducing experimental trends while resolving their molecular origins, these ensembles substantially narrow the longstanding simulation-experiment gap and provide a basis for engineering tethered-DNA devices.