A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2′-Deoxynucleotides

Abstract

The abiotic synthesis of ribonucleotides is thought to have been an essential step toward the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2′-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2′-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of riboand arabinonucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2′deoxy-or arabinonucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization

“…As previous reports suggest that nucleobase identity has little impact on the rate of formation of the imidazolium-bridged dinucleotide intermediate ( 25 , 26 ), we utilized 2AIptC as a model substrate, which allowed us to investigate intermediate formation at a much higher concentration. When we incubated purified 2AIptC at a concentration of 60 mM at pH 8 and followed the reaction by 31P-NMR, we found that the imidazolium-bridged TNA dinucleotide is formed, but the observed rate of 8.8 × 10 −4 h −1 mM −1 is approximately 4–5-fold slower than the corresponding rates for the activated ribonucleotides 2AI-rA and 2AI-rC (3.2 and 4.5 × 10 −3 h −1 mM −1 ) ( 26 , 27 ) (Figure 2D ). Nonenzymatic copying rates are dependent on multiple factors, including the rate of formation of imidazolium-bridged dinucleotide intermediates and their reactivities.…”

“…The largest deviations between the two structures are at the primer terminus, where the tG residue is shifted and twisted compared to the native RNA primer, with distances in the range of 1.5–2.4 Å between the corresponding atoms of the threose and ribose sugar rings (Figure 6E ). The tG residue has a glycosidic linkage torsion χ angle of –121° (Table 1 ), compared to a typical χ angle of –168° for the ribonucleotides of the primer ( 26 ).…”

Solvation and Stabilization of Single Strand RNA at the Air/ice Interface Support a Primordial RNA World on Ice

“…Moreover, in a water restricted environment such as the topmost layers of the air/ice interface, the bases would be more prone to base-stacking, enabling the correct base pairing with other free nucleotide that would be floating in the topmost part of the ice-QLL, where the water diffusivity is faster. 42 In addition, since the synthesis of building blocks for nucleotide synthesis has been shown to be plausible in prebiotic aqueous conditions, 14,[43][44] an immobilized and stretched out ssRNA on ice, as the one shown in Fig. 1b, could be more prone to polymerization and self-replication with free nucleotides diffusing in the ice-QLL than a compact arrangement in the absence of protein-assisted replicase.…”

“…11 Unresolved questions remain, however, about the emergence of prebiotic RNA and its evolution in the absence of protein-assisted biochemical mechanisms. Even granting abiotic formation of nucleotides in a prebiotic soup (a topic still intensely debated 6,[11][12][13][14], polymerization of nucleotides faces an uphill free energy gradient. 11 In addition, in aqueous solution at room temperature RNA polynucleotides degrade quickly 15 because the phosphodiester link between monomers is vulnerable to nucleophilic attack and breakage by the deprotonated 2'-OH group of the ribose sugar.…”

The virtual circular genome model for primordial RNA replication

“…The incorporation of an arabino-nucleotide into a growing oligonucleotide during primer extension is essentially a chain terminating event (Kim et al 2020). Such events would be fatal if genome replication required continuous end-to-end copying of a template strand.…”