Spin effects govern DNA/RNA nucleotide polymerization

Abstract

A new radical mechanism of nucleotide polymerization is found. The finding is based on the Car-Parrinello molecular dynamics computations at 310 K with an additional spin-spin coupling term for 31P and 1H atoms and a radical pair spin term included. The mechanism is initiated by a creation of a high-energy spin-separated Mg-ATP complex in a triplet state in which the Mg prefers an uncommon chelation to the O2-O3 oxygens of the ATP. The cleavage of the complex produces the AMP-and O-radicals. The latter captures a proton from acidic solution (the Zundel cation) that converts it into the OH radical. The process agrees with the protoncoupled electron transfer (PCET) mechanism. Through interacting with the HO-C3' group of the deoxyribose/ribose the OH radical captures its hydrogen atom. The process is accompanied by producing water and the AMP radical. The AMP-and AMP radicals then interact yielding a dimer. The described mechanism is easily generalized for a bigger number of adjoining nucleotides and their type. The radical mechanism is highly sensitive to the AMP-OH radical pair spin symmetry and the radius of the OH diffusion. This confines the operation of the radical mechanism: it is applicable to nucleotide polymerization through the HO-C3' group of deoxyribose/ribose (DNA/RNA polymerization) and inapplicable through the HO-C2' group of ribose (RNA)-a result that nature has developed over evolution.

Magnetic isotope and magnetic field effects on the DNA synthesis

“…At last, we would like to point out that some ion–radical mechanisms of spin-dependent synthesis of DNA/RNA were suggested by Tulub et al (26,27). Magnesium isotope effects on the growth of Escherichia coli cells as well as protective function of 25 Mg ions in the post-radiation recovery of the cells of yeast Saccharomyces cerevisiae enriched with 25 Mg ions were also detected (28–30).…”

Spin nature of genetic code

“…The CI passage produces a radical pair (RP)-NMP and OH ( stands for a radical)-which spin correlation determines the further elongation of the chain or termination of its growth. With the RP and its two spins in mind, we have a picture (Figure 1) that models the process of DNA/RNA nucleotide synthesis on the complementary DNA template and proves the necessity of a triplet nucleotide se- The initially created RP is in T state (two arrows, indicating spins, are up-directed) and their spins, for simplicity, rest on the G' nucleotide (actually, the spins are on G'MP and OH, see text and [4]). One electron spin migrates on the template (a small curved arrow).…”

“…C, T, U) decay to nucleosidemonophosphate (NMP) [6]. The Mg-NTP decay is spin-dependent [4]. It occurs at the conical intersection (CI) of the triplet (T) and singlet (S) potential energy surfaces (PESs) and assumes overcoming a potential barrier of 25.4 kcal/mol [4,5].…”

“…The Mg-NTP decay is spin-dependent [4]. It occurs at the conical intersection (CI) of the triplet (T) and singlet (S) potential energy surfaces (PESs) and assumes overcoming a potential barrier of 25.4 kcal/mol [4,5]. The CI passage produces a radical pair (RP)-NMP and OH ( stands for a radical)-which spin correlation determines the further elongation of the chain or termination of its growth.…”

“…The paper aims to shed light on why genetic code is triplet. The answer is rooted in recently found short-living spin nature of nucleotides [4,5].…”