Influence of Dielectric Constant on Codon-Anticodon pairing in mRNA and tRNA triplets by Theoretical Studies: Hartree-Fock and Density Functional Theory Calculations.

Abstract

In this paper we have focused on the dielectric constant effect between various solvents with theoretical model<br />in the biochemical process. Thereby, AAA, UUU, AAG and UUC triplex sequences have been optimized in<br />water, methanol, ethanol and DMSO with proposed SCRF Model of theory. The solvation of biomolecules is<br />important in molecular biology since numerous processes involve to interacting a protein with changing of<br />solvent-molecule.<br />The hydrogen bond is one of the important predictions of structural and functional in biochemical and<br />biophysical of biological complexes such as proteins. mRNA-tRNA pairing as a fundamental step in protein synthesis is a complexes process controlled by hydrogen bonding between two anti-parallel trinucleotides,<br />namely the mRNA codon and the tRNA anticodon.<br />In order to determine the optimized structural biology including of bond lengths, bond angles and dihedral<br />angles energies, dipole moments and other properties of codons and anticodon, we have performed ab initio<br />calculations of Quantum Mechanics (QM) at HF/sto-3G, 3-21G, 6-31G levels in gas phase and a few solvents<br />with different dielectric constans via the SCF method using the GAUSSIAN 98 software package. Optimization<br />at the HF/6-3 1G level has yielded results in better agreement with the experimental data.