Unveiling the dynamic biomechanical landscape of DNA origami nanotubes: insights from steered molecular dynamics at Varied temperatures and stretching rates

DNA origami nanotubes (DONs) hold significant promise in nanotechnology and biomedicine. Understanding their mechanical properties and response to environmental factors is essential for realizing their potential. Here, we employed steered molecular dynamics (SMD) simulations to investigate the mechanical characterization of a designed DON under simulated varied temperatures and stretching rates. A DON was designed and modeled using caDNAno software and GROMACS facilitated SMD simulations to explore its elasticity across a temperature range of 290-370K, maintaining a constant stretching rate of 0.05 nm/ps for 120 ps. Additional simulations were conducted at three distinct stretching rates (0.01, 0.05, and 0.1 nm/ps) at 310 K. Also, Young's modulus analysis evaluated the nanotube's elasticity. Structural variations in the DON were observed under changing temperatures and stretching rates. Remarkably, the nanotube exhibited higher stiffness at 0.1 nm/ps compared to the default 0.05 nm/ps stretching rate, closely approximating values at 310K. This investigation offers valuable insights into the mechanical behavior of DONs, contributing significantly to the progress of nanoscale engineering and DNA nanotechnology.