Recognition of the wobble pair: quantum mechanical calculations of tRNA U34 or C34 modifications within the ribosomal...

Uracil at position 34 of transfer RNAs (tRNAs) is generally modified and can recognize G + 3 via two geometrically different pairs, anionic or tautomeric. We sequentially calculated the thermodynamic parameters of isolated U•G pairs in geometrically different states modified with s2U, mnm5U, mcm5U, mnm5s2U, and mcm5s2U, and found that the modifications differently influence their state transition energy (isomerization) and base pairing strength, thereby their formation. Both mnm5U•G and mnm5s2U•G pairs occur as the anionic or tautomeric form and the zwitterionic state is preferred. When tautomeric, the mcm5s2Uenol state is thermodynamically preferred. After geometrical optimization within the structurally determined decoding environment, the quantum mechanical calculations reveal that, depending on the modification, additional H-bonds are formed within or outside the anticodon loop. Collectively, the modifications at 34 affect the electronic states (anionic or tautomeric) of the modified bases and lead to specific isosteric geometries of the wobble pairs within the decoding complexes. Slight variations in the ribose pucker of G3 gives enough mobility for its base part to differently pair with the modified U34. The structural and theoretical data converge to show that these factors act jointly for preorganizing the geometry-based recognition at the wobble position toward an efficient and accurate translation.