Dependence of nucleotide physical properties on their placement in codons and determinative degree

TL;DR

This study investigates how nucleotide physical properties vary depending on their position within codons and their determinative degree, using computational methods that account for neighbor interactions.

Contribution

It introduces a novel analysis of nucleotide properties considering codon position and determinative degree, incorporating neighbor interactions in the calculations.

Findings

Physical properties vary with codon position and determinative degree.

Differences observed between codons and anticodons.

Neighbor interactions influence nucleotide property calculations.

Abstract

Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (Austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependences of these variables from the place in the codon and the determinative degree were obtained. The difference of these variables for codons and anticodons is shown.