Making Molecules with Clay: Layered Double Hydroxides, Pentopyranose Nucleic Acids and the Origin of Life.

Harold Bernhardt

doi:10.3390/life9010019

Abstract

A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing—and therefore information transfer—has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA. Pentose diphosphates comprise the backbone monomers of pentopyranose nucleic acids, some of the strongest base pairing systems so far discovered. We have previously proposed that the first base pairing interactions were between purine nucleobase precursors, and that these were weaker and less specific than standard purine-pyrimidine interactions. We now propose that the inherently stronger pairing of pentopyranose nucleic acids would have compensated for these weaker interactions, and produced an informational polymer capable of undergoing nonenzymatic replication. LDH clays might also have catalysed the synthesis of the purine nucleobase precursors, and the polymerization of pentopyranose nucleotide monomers into oligonucleotides, as well as the formation of the first lipid bilayers.

Highlights

Demonstrating the potential utility of a unified ‘systems chemistry’ approach to the problem of the origin of life, Powner and colleagues [1,2,3] recently proposed a link between a plausible early metabolic pathway and amino acid synthesis, through reactions between the small aldehyde phosphates glycolaldehyde phosphate (GAP) and glyceraldehyde-2-phosphate (G2P)
One of these—ribose-2,4-diphosphate—constitutes the backbone subunit of pyranosyl-RNA [5], a pentopyranose nucleic acid that differs from RNA only in the position of its phosphate groups on the ribose ring, and in the ribose ring being six-membered (Figure 1)
We have previously proposed that the prebiotic synthesis of RNA

Summary

Introduction

Demonstrating the potential utility of a unified ‘systems chemistry’ approach to the problem of the origin of life, Powner and colleagues [1,2,3] recently proposed a link between a plausible early metabolic pathway and amino acid synthesis, through reactions between the small aldehyde phosphates glycolaldehyde phosphate (GAP) and glyceraldehyde-2-phosphate (G2P). One of these—ribose-2,4-diphosphate—constitutes the backbone subunit of pyranosyl-RNA [5], a pentopyranose nucleic acid that differs from RNA only in the position of its phosphate groups on the ribose ring, and in the ribose ring being six-membered (as opposed to five-membered as it is in RNA) (Figure 1). The four pentopyranose phosphate systems with 40 →20 -backbone connectivity (including pyranosyl-RNA and α-arabinopyranose nucleic acid) are able to base pair with each other; in contrast, none of the four form base pairs with RNA. Life 2019, 9, 19 connectivity (including pyranosyl-RNA and α-arabinopyranose nucleic acid) are able to base pair with each other; in contrast, none of the four form base pairs with RNA.

Nucleic acid backbone showingofposition of groups phosphate attached

PO and PO4 within their

24 Å in order to accommodate able more thanable triple width from

Computer simulation snapshot ofinteraction the interaction between an 25-mer

Findings

Hypothesis