Preferences of AAA/AAG codon recognition by modified nucleosides, τmsU and tA present in tRNA.

Deficiency of 5-taurinomethyl-2-thiouridine, τmsU at the 34th 'wobble' position in tRNA causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNA, recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level. Hence, multiple MD simulations of various molecular models of anticodon stem loop (ASL) of mt tRNA in presence and absence of τmsU and N-threonylcarbamoyl adenosine (tA) along with AAA and AAG codons have been accomplished. Additional four MD simulations of multiple ASL mt tRNA models in the context of ribosomal A-site residues have also been performed to investigate the role of A-site in recognition of AAA/AAG codons. MD simulation results show that, ASL models in presence of τmsU and tA with codons AAA/AAG are more stable than the ASL lacking these modified bases. MD trajectories suggest that τmsU recognizes the codons initially by 'wobble' hydrogen bonding interactions, and then tRNA might leave the explicit codon by a novel 'single' hydrogen bonding interaction in order to run the protein biosynthesis process smoothly. We propose this model as the 'Foot-Step Model' for codon recognition, in which the single hydrogen bond plays a crucial role. MD simulation results suggest that, tRNA with τmsU and tA recognizes AAA codon more preferably than AAG. Thus, these results reveal the consequences of τmsU and tA in recognition of AAA/AAG codons in mitochondrial disease, MERRF.