Predicting nearest neighbor free energies of modified RNA with LIE: Results for pseudouridine and N1-methylpseudouridine within RNA duplexes

Pseudouridine and N1-methylpseudouridine are the key modifications in the field of mRNA therapeutics and vaccine research. The accuracy of the design and development of therapeutic RNAs containing such modifications requires the accuracy of the secondary structure prediction, that depends on the nearest neighbor (NN) thermodynamic parameters for the standard and modified residues. The development of such NN thermodynamic parameters requires expensive and time-consuming experimental studies. There were some earlier attempts to predict the NN free energies of modified RNA using computational methods but those are either computationally expensive or not accurate enough. Here, we propose a new protocol based on MD simulations, which is able to predict the NN free energy parameters (ΔG◦37) for U-A, Ψ-A and m1Ψ-A pairs in general agreement with the recent experimental reports. We report the NN thermodynamic parameters for different U, Ψ and m1Ψ base pairs, which might be helpful for a deeper understanding of the effect of these modifications in RNA. The presence of m1Ψ resulted in more stable NN pairs compared to those containing U or Ψ. The predicted NN free energy parameters in this study are able to closely reproduce the folding free energies of duplexes containing internal Ψ for which the thermodynamic data were available. Additionally, we report the predicted folding free energies for the duplexes containing internal m1Ψ.