Quantum chemical considerations on degeneracy of the genetic code: Anticodon-codon wobble base pairing

The wobble hypothesis suggested by Crick explains the general nature of the degeneracy of the genetic code. Recently the question of the extent to which the configuration of a solitary base pair may determine whether it will occur at the wobble position or not was addressed [G. Das, R.H.D. Lyngdoh, J. Mol. Struct. (THEOCHEM) 851 (2008) 319]. The present theoretical study is intended to address the same question and to define the limits of flexibility required to rule out or accept a candidate wobble pair at a higher computational level. Eight bases (acting as the anticodon wobble base) are made to pair via H-bonding with four major RNA bases (acting as the codon wobble base). This study presents optimized structures of dozens of base pairs and their binding enthalpies, ranging from −5.1 to −26.4 kcal/mol at the B3P86/6-311++G** level of calculation. It is found that neither the charge transferred between the components of a base pair nor binding enthalpy is a decisive factor for the occurrence of a given pair. However, the latter have, on average, a significantly higher value for the allowed pairs than for the non-allowed ones. For the base pairs several configuration markers are evaluated and tabulated; one of them, the local planarity parameter, is proposed here for the first time. It mirrors the local planarity of a base pair in the domain of hydrogen bonds. Values of these markers screen effectively between experimentally observed and unobserved pairs for all of the cases examined here but one.