NMR and Solvent Effect Study on the Thymine-Adenine-Thymine Sequence: A Theoretical Investigation on chemical behavior of Nucleotides in solution

Abstract

In our current research, we have taken into account nuclear shielding parameters of Thymine-Adenine-Thymine (TAT) sequence using GIAO and Self-Consistent Reaction Field (SCRF) method at the level of HF/ 3-21G theory both in the gas phase and in different solvents such as water, ethanol, methanol, nitromethane and DMSO. These solvents represent a wide range of solvent propertis from the point of view of polarity as well as hydrogen bonding interactions. Our results reveal that NMR chemical shielding parameters are strongly affected by inducing different solvent media. Regarding to our plotted graphs of σiso and ΔE relatives versus є, the lowest σiso values obtained in methanol for nitrogen atoms. However, the opposite trend yielded for the graph of asymmetry parameter (η) versus є. Hydrogen bonding environment strongly affects the chemical shielding tensors and orientation of nuclei. It is noteworthy that the small variation in the position of atoms, eventually yields considerable change in the NMR shielding tensors of the various intermolecular hydrogen bonds. So, solute to solvent hydrogen-bonding effects on the calculated NMR shielding tensors has been concerned. According to our theoretical results of energy values, some important relationships have been found between the dielectric constant and structural stability of TAT sequence. For further evidences, we have discussed about the plotted graphs of relative energies versus dielectric constants of our considered solvents. Thus, we can drastically conclude that the dielectric permittivity of the solvent is a key factor that determines the chemical behavior of DNA in solution.

Keywords: TAT sequence; solvent effect; NMR parameters; Ab initio

Egyptian Journal of Biochemistry and Molecular Biology Vol. 26 (1) 2008 pp. 83-100