The LEaP module in AMBER20 was used to set up the simulation box with UBP-incorporated DNA duplex in water. Neutralization of the system with the required number of counterions (Na + ), and solvation of the system in a cubic box filled with TIP3P water , extending at least 12 Å from the DNA duplex was done with the LEAP module in AMBER. All MD simulations were performed with the AMBER20 pmemd.cuda program using the Ol15 AMBER force field. Seven minimization steps were done with decreasing restraint (10.0-0.0 kcal mol-1 Å -2 ) on the solute's heavy atoms. In each stage, the system was minimized with 5000 cycles of minimization of steepest descent, followed by 5000 cycles of conjugate gradient minimization. Subsequently, each system was heated to 300 K using Langevin dynamics with a collision frequency of 2 ps -1 followed by 7 ns of NVT equilibration with decreasing restraints (10.0-0.0 kcal mol -1 Å -2 ) on the system's heavy atoms every ns. Production calculations for each system were performed for 1 µs in the NPT ensemble without