A 500 MHz proton NMR study of stacking interactions: binding of tripeptide Lys-Tyr-Lys to tetradeoxynucleotide d-GpCpGpC

The complete sequential assignment and conformation of d-GpCpGpC in D2O has been determined from 1D NMR spectra at 285-320 K and room temperature 2D-COSY and NOESY spectra. The tetradeoxynucleotide exists primarily as a right handed double helix at 285 K, having Tm as 314 K. On binding to a tripeptide Lys-Tyr-Lys in a concentration equimolar to tetranucleotide duplex, the Tyr ring protons shift upfield by 0.14 ppm at 285 K. The increase in Tm on binding suggests stabilization of duplex. The existence of intermolecular NOEs between C4 sugar protons and Tyr alpha C and Lys alpha C protons give direct evidence of proximity of Tyr residue to the C4 base of d-GpCpGpC. The conformation of d-GpCpGpC remains unchanged on binding. The observed results are interpreted in terms of preferential stacking of aromatic ring of Tyr residue with proximal base-pair of d-GpCpGpC, stabilized by electrostatic interaction of Lysine side chains with backbone phosphates. This is in contrast to intercalculation of aromatic dyes within base-pairs resulting in a change in sugar conformation at the binding site.