1H-NMR studies on association of mRNA cap-analogues with tryptophan-containing peptides

1 H-NMR spectroscopy was applied to a study of the mode of interaction, in aqueous medium in the pH range 5.2–8.5 and at low and high temperatures, between several mono- and dinucleotide analogues of the mRNA cap m 7 GpppG and a selected tripeptide Trp-Leu-Glu, and a tetrapeptide Trp-Glu-Asp-Glu, the sequence of which corresponds to one of the suspected binding sites in the MRNA cap-binding protein (CBP). A program, GEOSHIFr, was developed, based on ring-current anisotropy theory, for analysis of experimentally observed changes in chemical shifts accompanying interactions between aromatic heterocyclic rings. This permitted quantitative evaluation of stacking interactions between the m 7 G cap and the tryptophan indole ring, and the relative orientations of the planes of the two rings, spaced about 3.2 A apart. The structures of the stacked complexes were determined. In particular, stacking between m 3 2,2,7 G (which has no free amino group for hydrogen bonding) and the indole ring is weaker and quite different from that between m 7 G and m 2 2,7 G and indole. With the dinucleotide cap-analogues, only the m 7 G component stacks with the indole ring, without disruption of intramolecular stacking. In contrast to numerous earlier reports, the calculated stacking interactions are quantitatively in accord with the values derived from fluorescence measurements. It also has been shown that the positively charged (cationic) form of m 7 G stacks much more efficiently with the indole ring than the zwitterionic form resulting from dissociation of the guanine ring NlH (p K a ≈ 7.3).