Molecular interactions of 2′-deoxyguanosine 5′-monophosphate with glycine in aqueous media probed via concentration and pH dependent Raman spectroscopic investigations and DFT study

Abstract

In order to gain insights into nucleotide–protein interaction, the molecular interaction of glycine (Gly) with 2′-deoxyguanosine 5′-monophosphate (dGMP) was monitored in aqueous media through Raman spectroscopic measurements and density functional theory (DFT) calculations. Raman spectra of dGMP, glycine and their binary mixtures (dGMP + Gly) in aqueous media at 10 different concentrations corresponding to the dGMP : Gly molar ratios varying from 1 : 1 to 1 : 10 were recorded in the fingerprint region 2000–400 cm⁻¹. Raman spectra of the dGMP : Gly mixture with a molar ratio of 1 : 3 in aqueous media at 10 different pH values starting from 1 to 10 at an interval of 1 were also recorded. The DFT calculations were performed on dGMP, glycine and their various complexes with varying number of H₂O molecules in gas phase as well as in solvation using hybrid functional B3LYP employing the high level basis set 6-311+G(d,p). The variations in the observed spectral features were explained in terms of calculated optimized structures of dGMP, glycine and their various complexes with water molecules and a good spectra–structure correlation was obtained. Raman spectra of glycine in 1.2 M aqueous solution were also recorded at three pH values, 2, 6 and 10, and the subtle differences in the spectral features were correlated with the calculated Raman spectra of protonated, deprotonated and zwitterionic forms of glycine. The results also give experimental evidence rather convincingly that the zwitterionic and protonated forms of glycine are formed at pH = 6 and 2, respectively, but even at pH = 10, deprotonated glycine is not formed. An important aspect of this study is the monitoring of the interaction of dGMP with the zwitterionic form of glycine giving insightful details regarding the binding site.