Characterization of Thermodynamic Properties of RNA Modifications: Inosine and Pseudouridine

Inosine (I) and pseudouridine (Ψ) are naturally occurring RNA modifications that may be found on tRNA, mRNA and other RNA types. These modifications play several roles in cell biology and dynamics. Inosine can be recognized by cell machinery as a guanosine, leading to epigenetic variability during protein synthesis. Pseudouridine is a uridine isomer, which is associated with higher RNA duplex stability and plays a role in stabilizing all tRNA. This type of RNA modification may lead to biotechnological applications such as RNA vaccines and mismatch repair for RNA probes. Although RNA modifications are already in use for several purposes, little is known about their thermodynamic contribution to RNA duplex stability. In this work, we used the Peyrard-Bishop (PB) mesoscopic model to evaluate the thermodynamic contribution of inosine and pseudouridine modifications in RNA. With this model we obtained hydrogen bond and stacking parameters of RNA sequences containing at least one inosine or one pseudouridine. We found that inosine is able to stabilize RNA duplexes although IU and IC hydrogen bonds are much weaker than AU and GC canonical pairs. In contrast, the results about pseudouridine show that ΨA pairs have hydrogen bonds stronger than AU pairs, while ΨU and ΨG mismatches have hydrogen bonds weaker then their canonical analogs (AU and CG). Our findings show that both IU and IC pairs may stabilize RNA duplexes, although less than AU and CG pairs. Also there is a contribution from pseudouridine to the stabilization of RNA duplexes, especially the ΨA pair which has hydrogen bonds stronger than canonical AU pairs.