Our simulations also allowed to demonstrate that replacing oxygen with sulfur in uridine enhances the binding of activated adenosine dinucleotides. Consequently the ApAIpA:tUtU system exhibits somewhat higher binding specificity through Watson-Crick base pairing interactions that its counterpart containing biological U nucleotides within the template. This result is qualitatively consistent with the experimental improvement of the yield and fidelity of the reaction with tU nucleotides, however, the simulations do not indicate a substantial increase, which is otherwise seen from the experiments . Furthermore, MD of the opposite system containing the tUpAIptU dinucleotide bound to the AA template resulted in less specific binding than in the case the UpAIpU. This inconsistency between the experimental result and the simulations may arise from various factors, including potential deficiencies and limitations of the classical RNA force field in accurately describing the binding of imidazolium-bridged dinucleotide intermediates on the RNA template, especially when they consist of non-standard and newly parameterized residues, which were not extensively tested so far. Therefore, we underscore that our classical MD simulations offer very valuable qualitative insights into the process on the molecular level. Nevertheless, a more picture would require the application of more accurate methods of quantum chemistry, which are often limited by very unfavorable scaling with the system size.