The hypermodified Y base electrostatic contribution to the energetics of the codon-anticodon pairing in tRNAPhe

We report ab initio results at the Hartree-Fock/6-31G level for the energetics of the codon-anticodon pairing in tRNA(Phe). We have employed a molecular dynamics protocol in order to relax the studied crystallographic structure. Electrostatic potentials due to the presence of the hypermodified Y base and a guanine base in position 37 of the anticodon loop are compared. The results of the electrostatic potentials on the planes containing the molecules of the complementary codon bases UUC, indicate a strong energetic stabilization when a Y base is present, in comparison to the substitution by a guanine base. The present results provide some molecular data on the energetics of the codon-anticodon pairing mechanism and are related to experimental studies which suggest that hypermodification in tRNAs contribute to the regulation of gene expression. (C) 1998 Elsevier Science B.V.