Mechanical Rupture of DNA Tension-Gate Elements: Thresholds, Kinetics, and Energetics from Steered Molecular Dynamics

The kinetics and energetics of load-driven conformational rearrangements underlie DNA replication, repair, and DNA nanodevice function. DNA tension-gate tethers exploit these dynamics, yet their rupture thresholds are set almost exclusively by single-molecule calibration; here, an atomistic steered-molecular-dynamics pipeline predicts relative thresholds and characterizes the underlying rearrangements. Seven constructs—duplexes of varying length and GC content, single-stranded poly(dT)30, a GC-clamped hairpin, and G-quadruplex—were pulled with 50 trajectories per construct per rate (0.01/0.001 nm/ps). At MD loading rates, the ordering G-quadruplex (911 pN) > GC-rich duplex (786 pN) > hairpin (643 pN) > mixed duplexes (559/558 pN) > ssDNA (388 pN) holds at both rates, and the design rules deconfound, +68 pN for GC content (47% → 100%), −160 pN for doubled length, and 208 pN for pull geometry—larger than GC itself. Dissipated work falls 31–58% at the slower rate; slow-rate Jarzynski estimators converge for low-dissipation elements, while fast-rate profiles of high-dissipation motifs do not. Absolute thresholds at experimental rates remain out of reach, but the ordering—the actionable output for TGT design—comes with transferable structure-gating and convergence-diagnostic protocols, positioning atomistic simulation as a quantitative complement to single-molecule spectroscopy.