Explicit Solvent Molecular Dynamics (MD) Simulations.

The simulations were carried out with AMBER 16³⁹ simulation package using the revised χ³² and α/γ³¹ torsional parameters, which we call RNA-IL. A second set of simulations were carried out using the ff99OL3 force field, which uses the ff99 force field⁴⁰ with parmbsc0 α/γ⁴¹ and σ_OL3³⁰ modifications. The nucgen module of AMBER 16 was utilized to build the initial structures in A-form for each RNA DNMP (AA, AC, AG, AU, CA, CC, CG, CU, GA, GC, GG, GU, UA, UC, UG, UU). Each system was first neutralized with a single Na⁺ ion⁴², which then was solvated with 2000 TIP3P⁴³ water molecules in a truncated octahedral box with periodic boundary conditions. Each system was then augmented with five Na⁺ and Cl⁻ ions to mimic physiological conditions, where after equilibration each system had 0.162 M Na⁺ concentrations. The structures were first minimized and then equilibrated in two steps as described before.⁴⁴ After minimization and equilibration, a 10 μs MD simulation with the RNA-IL and ff99OL3 force fields with a 2 fs time step was performed for each system using NPT dynamics with isotropic positional scaling and Berendsen barostat. The reference pressure was set to 1 atm with a pressure relaxation time of 2 ps. SHAKE⁴⁵ was turned on for constraining bonds involving hydrogen atoms. An atom-based long-range cutoff of 8.0 Å was used in the production runs. The reference temperature was set to 300K. PME was used to handle the electrostatics.⁴⁶ The Langevin thermostat^47–48 was applied with a coupling constant γ = 1.0 ps⁻¹.