A 500 MHz proton NMR study of the interaction of the tripeptide Lys-Tyr-Lys with the tetradeoxynucleotides d-CpCpGpG and d-CpGpCpG

Two dimensional proton NMR experiments at 500 MHz show that d-CpCpGpG exists as a right handed B-DNA structure in D2O solution with both sugars in O1' endo and glycosidic bond angle in anticonformation. On complexation with tripeptide Lys-Tyr-Lys, it forms a well characterized complex with two identical strands. The Tyr ring protons shift upfield by about 0.07p.p.m. at 285 K due to stacking with base pairs. This is accompanied by changes in chemical shift of base protons and the melting temperatureT m with practically no change in conformation of tetranucleotide. All changes in chemical shift decrease with temperature. Interaction of d-CpGpCpG with Lys-Tyr-Lys leads to a comparatively large upfield shift of Tyr ring protons, being ~0.14 p.p.m. at 285 K followed by stabilisation of double helix. A comparison of the interaction of tripeptide with different di- and tetranucleotides shows that the interaction decreases in the order d-GpCpGpC > d-CpGpCpG > d-CpCpGpG > d-GpC > d-CpG apparently suggesting that Tyr ring stacks preferentially in 5'-GpC 3' site. Such findings have important implications in protein-nucleic acid interactions