In this contribution, we expanded our previous studies and determined the structural ensemble adopted by 2×2 GG/GG and 2×2 CC/CC internal loops. Recent advances in NMR spectroscopy have provided the opportunity to validate the existence of transiently formed low populated conformations, adding to the repository of structural candidates that can be targeted by small molecules. Despite these advances, it is almost impossible to capture all the possible conformations via current experimental approaches. Therefore, we combined molecular dynamics (MD) calculations with NMR experiments, including the use of site-specific modified RNA residues, to determine the conformational states of 2×2 GG/GG and 2×2 CC/CC.