Spin nature of genetic code

Abstract

Nature has developed codon as a tool to manipulate a two-electron spin symmetry (short-living electrons, forming a radical pair, arise from the Mg-bound nucleosidetriphosphate cleavage at the triplet/singlet (T/S) crossing), which permits or forbids further nucleotide synthesis (DNA/RNA) and the synthesis of proteins. The thesis is confirmed by conducting DFT:B3LYP (6-311G** basis set) computations (T/S potential energy surfaces) with the model system composed of the template (C-G-C-G-A nucleotide sequence) and the growing chain (G-C-G nucleotide sequence, DNA or RNA). The origin of codon is in hyperfine interaction between a single electron, transferred onto the template, and three 31P nuclei built into the phosphorus fragments of nucleotides. The nuclei, together with the polynucleotide structure, form a spiral twist that is homeomorphic to a triangle patch on the Poincare sphere. Each triangle has unique angle values depending on the nucleotide nature and their position in the codon. The patch tracing produces the Berry phase changing the electron spin orientation from “up” to “down”. The Berry phase accumulation proceeds around the (T/S) conical intersections (CIs). The CIs are a result of complementary recognition between nucleotide bases at distances exceeding the commonly accepted Watson-Crick pairing by 0.17 A. Upon changing spin symmetry, the DNA or RNA chain is allowed to elongate by attaching a newly coming nucleotide. Without complementary recognition between the bases, the chain stops its elongation. The Berry phase accumulation along the patch tracing explains the effect of Crick’s wobbling when the second nucleotide plays a primary role in recognition. The data is directly linked to creation of a quantum computing device.