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

Subject Areas : Journal of Physical & Theoretical Chemistry

M. Monajjemi ¹ , M.H. Razavian ² , F. Mollaamin ³ , F. Naderi ⁴ , H. Monajemi ⁵ , S. Saki ⁶ , R.A. Khavari-nejad ⁷ , K.Zare Zare ⁸ , A. Haddadi ⁹

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Received: 2015-05-03 Accepted : 2015-05-03 Published : 2007-02-01

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Abstract :

In this paper we have focused on the dielectric constant effect between various solvents with theoretical modelin the biochemical process. Thereby, AAA, UUU, AAG and UUC triplex sequences have been optimized inwater, methanol, ethanol and DMSO with proposed SCRF Model of theory. The solvation of biomolecules isimportant in molecular biology since numerous processes involve to interacting a protein with changing ofsolvent-molecule.The hydrogen bond is one of the important predictions of structural and functional in biochemical andbiophysical 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,namely the mRNA codon and the tRNA anticodon.In order to determine the optimized structural biology including of bond lengths, bond angles and dihedralangles energies, dipole moments and other properties of codons and anticodon, we have performed ab initiocalculations of Quantum Mechanics (QM) at HF/sto-3G, 3-21G, 6-31G levels in gas phase and a few solventswith different dielectric constans via the SCF method using the GAUSSIAN 98 software package. Optimizationat the HF/6-3 1G level has yielded results in better agreement with the experimental data.