Origins of life: Conformational energy calculations on primitive tRNA nestling an amino acid

Abstract

We report conformational energy calculations on our proposal of a molecular interaction theory for the origin of the nucleic acid-directed, adaptor-mediated synthesis of proteins that links the phenomena of chemical and biological evolution. A particular conformation of a pentanucleotide turns out to be a double-sided template for a primitive decoding system. It is able to neatly nestle an amino acid via hydrogen bonds, and this complex is found to be an energetically favourable conformation. The total potential energy of the complex is calculated using semi-empirical potential energy functions. A local-minimum conformation is obtained and its features are reported. The template conformation of the pentanucleotide is found to have an energy value far lower than a regular helical conformation. When the amino acid is nestled in the cleft of the template-conformation through specific hydrogen bonds, the energy is further lowered. A D-amino acid nestled into the PIT (Primitive tRNA) is found to be less stable than its L counterpart, as revealed by energy calculations.