The initial structure for this study was sourced from an article by Zhang et al. [PDB:6C8K]. Hypoxanthine and 2-thiouracil were parameterized according to the protocol given in the Supporting Information Section 2. Each system was solvated in truncated octahedral water box (SPC/E water model )with minimal distance between RNA molecule and border set up to 12 . To the solution were added 25 K + counterions for neutralization and 0.15M of KCl (Joung and Cheatham parameters ). The AMBER parmOL3 force field was applied, and an equilibration protocol was used. Initially, 500 steps of steepest descent minimization and 500 steps of conjugate gradient minimization were performed with 25 kcal•mol -1 position restraints on the RNA atoms. Subsequently, the system was heated to 300K, starting at 100K, with 25 kcal•mol -1 restraints during a 100 ps molecular dynamics simulation at constant volume. The third step involved minimization with 5 kcal•mol -1 , 500 steps of steepest descent and 500 steps of conjugate gradient minimization. Following this, a 50 ps equilibration was conducted with 5 kcal•mol -1 restraints, at a constant temperature of 300K and pressure of 1 bar. These last two steps (minimization and equilibration) were repeated for 4, 3, 2, and 1 kcal•mol -1 restraints. The final equilibration included 0.5 kcal•mol -1 position restraints on the solute molecule. The final molecular dynamics simulation was performed for 50 ps at constant temperature 300K and pressure 1 bar, without any constraints. The production runs were divided into 3 different simulations for every system, with randomized initial conditions and each production simulation was performed for 500 ns. Consequently, it gave 1.5 µs of simulation time for each system. All of the production simulations were performed at 300K and 1 bar with use of the Langevin thermostat and the Monte Carlo barostat . The hydrogen mass repartitioning , SHAKE and SETTLE algorithms were applied to allow setting time step to 4 fs as indicated by Hopkins Chad W., et al. . The cuttoff for non-bonding interactions was setl to 9. The CUDA accelerated pmemd module of AMBER22 was used to perform molecular dynamics production simulations.