All simulations with the polarizable AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular) force field were performed with the TINKER HP software. The systems were built using the packmole software. Initially, UBP-incorporated DNA duplex complex was minimized using the BFGS nonlinear optimization algorithm with a convergence criterion (RMS gradient) of 0.1 Å. Subsequently, relaxation via MD in vacuum followed by implicit water with the GBSA model for 2 ns to obtain the starting system was performed. After that the structure was solvated in explicit water in the center of a box with volume 50X50X50 Å 3 containing 24000 water molecules, and neutralized using packmole. Subsequently, the system was heated to 300 K in 4 simulation steps (2 ns each) with an NVT ensemble removing all positional restraints (100.0-0.0 kcal/ Å -1 ). After the equilibration step, MD simulations were carried out for 125 ns in an NPT ensemble (1 atm and 298 K) for 3 replicates each (total simulation time 375 ns). The Monte Carlo barostat and Bussi thermostat were used to maintain the pressure and temperature fixed respectively. The duration of the time step was 2 fs using RESPA integrator. The smooth particle mesh Ewald (PME) method was used in the calculation of charge, atomic multipole, and polarization interactions. A cutoff of 10 Å was used for van der Waals potential energy interactions and the real-space distance cutoff in the Ewald summation. 70