Atomic-level insights into nanoclay for prebiotic nucleoside phosphorylation

Abstract

Kaolinite nanoclay has long been recognized as playing a key role in the origin of life. However, the interaction of kaolinite (Kaol) with biomolecules in prebiotic chemistry and its catalytic mechanism still remain a great challenge. Herein, we comprehensively investigate the nucleoside interactions and phosphorylation processes on Kaol surfaces by a combination of wet-dry cycle experiments and first-principles calculations. The experimental results show that Kaol is able to promote the phosphorylation reactions of four typical nucleosides, but there are differences in the catalytic ability for different nucleosides. In this study, we considered two physicochemically different Kaol end-surfaces—the aluminium-hydroxyl surface (Kaol(001)) and the silica-oxygen surface (Kaol(00 1¯))—and find that Kaol(001) forms strong hydrogen bonds with the nucleoside, stabilizing the nucleoside that significantly reduces the kinetic barrier to phosphorylation. Moreover, ab initio molecular dynamics (AIMD) simulations showed that the Kaol(001)-nucleotide system is kinetically stable, highlighting its potential in protecting the reaction sites of prebiotic molecules and providing strong evidence for the role of Kaol in prebiotic chemistry.