Probing the influence of hypermodified residues within the tRNA3Lys anticodon stem loop interacting with the A-loop primer sequence from HIV-1

Replication of the HIV-1 virus requires reverse transcription of the viral RNA genome, a process that is specifically initiated by human tRNA₃^Lys packaged within the infectious virion. The primary binding site for the tRNA involves the 3′ 18 nucleotides with an additional interaction between an adenine rich loop (A-loop) in the template and the anticodon stem–loop region of the tRNA₃^Lys. The loop of the tRNA primer contains two hypermodified base residues and a pseudouridine that are required for a proper binding and activity. Here, we investigate the influence on the structure, dynamics and binding stability of the three modified residues (mnm⁵s²U34, t⁶A37 and Ψ39) using extensive molecular dynamics and Quantum Theory of Atoms in Molecules (QTAIM) analysis. Consistent with experiment, the results suggest that the three modified residues are required for faithful binding. Residues mnm⁵s²U34 and Ψ39 have a major influence in stabilizing the anticodon loop whereas mnm⁵s²U34 and t⁶A37 appear to stabilize the formation of the complex of tRNA₃^Lys with the HIV-1 A-loop.