A Prebiotic Ribosylation of Pyrimidine Nucleobases Enabled by Metal Cations and Clay Minerals

We report a prebiotically relevant solution to the N1-ribosylation of pyrimidine nucleobases, a well-known challenge to the RNA world hypothesis. We found that the presence of metal cations and clay minerals enable the previously unachievable direct ribosylation of uracil. Spectroscopy and chromatography analyses confirmed the formation of ribosylated uracil. The method can be extended to the ribosylation of 2-pyrimidinone. These findings are also compatible with the metal-doped-clay model, developed by our lab for the unified route of the selection of ribose and subsequent syntheses of nucleotide and RNA.

A Prebiotic Ribosylation of Pyrimidine Nucleobases Promoted by Metal Cations and Clay Minerals

We report a prebiotically relevant solution to the N1-ribosylation of pyrimidine nucleobases, a well-known challenge in the RNA World hypothesis. It is found that the presence of metal cations and clay mineral enables the previously unachievable direct ribosylation of uracil, providing by far the highest yield. Spectroscopy and chromatography analyses confirmed the formation of ribosylated uracil. The method can also be extended to the ribosylation of 2-pyrimidinone. These findings are also compatible with the metal-doped-clay model developed by our lab for the unified route of the selection of ribose and subsequent syntheses of nucleotide and RNA.

Depsipeptide nucleic acids: prebiotic formation, oligomerization, and self-assembly of a new candidate proto-nucleic acid

The mechanism by which genetic polymers spontaneously formed on the early Earth is currently unknown. The RNA World hypothesis implies that RNA oligomers were produced prebiotically, but the demonstration of this process has proven challenging. Alternatively, RNA may be the product of evolution and some, or all, of its chemical components may have been preceded by functionally analogous moieties that were more readily accessible under plausible early-Earth conditions. We report a new class of nucleic acid analog, depsipeptide nucleic acid, which displays several properties that make it an attractive candidate for the first informational polymer to arise on the Earth. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these depsipeptide nucleic acid oligomers are capable of complementary self-assembly, and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers may have been relatively facile.

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

<div>Outstanding questions about the RNA world hypothesis for the emergence of life</div><div>on Earth concern the stability and self-replication of prebiotic aqueous RNA.</div><div>Recent experimental work has suggested that solid substrates and low</div><div>temperatures could help resolve these issues. Here, we use classical molecular</div><div>dynamics simulations to explore the possibility that the substrate is ice itself. We</div><div>find that at -20 C, a quasi-liquid layer at the air/ice interface solvates a short (8-</div><div>nucleotide) RNA strand such that phosphate groups tend to anchor to specific</div><div>points of the underlying crystal lattice, lengthening the strand. Hydrophobic bases,</div><div>meanwhile, tend to migrate to the air/ice interface. Further, contacts between</div><div>solvent water and ribose 2-OH’ groups are found to occur less frequently for RNA</div><div>on ice than for aqueous RNA at the same temperature; this reduces the likelihood</div><div>of deprotonation of the 2-OH’ and its subsequent nucleophilic attack on the</div><div>phosphate diester. The implied enhanced resistance to hydrolysis, in turn, could</div><div>increase opportunities for polymerization and self-copying. These findings thus</div><div>offer the possibility of a role for an ancient RNA world on ice distinct from that</div><div>considered in extant elaborations of the RNA world hypothesis. This work is, to the</div><div>best of our knowledge, the first molecular dynamics study of RNA on ice</div>

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

<div>Outstanding questions about the RNA world hypothesis for the emergence of life</div><div>on Earth concern the stability and self-replication of prebiotic aqueous RNA.</div><div>Recent experimental work has suggested that solid substrates and low</div><div>temperatures could help resolve these issues. Here, we use classical molecular</div><div>dynamics simulations to explore the possibility that the substrate is ice itself. We</div><div>find that at -20 C, a quasi-liquid layer at the air/ice interface solvates a short (8-</div><div>nucleotide) RNA strand such that phosphate groups tend to anchor to specific</div><div>points of the underlying crystal lattice, lengthening the strand. Hydrophobic bases,</div><div>meanwhile, tend to migrate to the air/ice interface. Further, contacts between</div><div>solvent water and ribose 2-OH’ groups are found to occur less frequently for RNA</div><div>on ice than for aqueous RNA at the same temperature; this reduces the likelihood</div><div>of deprotonation of the 2-OH’ and its subsequent nucleophilic attack on the</div><div>phosphate diester. The implied enhanced resistance to hydrolysis, in turn, could</div><div>increase opportunities for polymerization and self-copying. These findings thus</div><div>offer the possibility of a role for an ancient RNA world on ice distinct from that</div><div>considered in extant elaborations of the RNA world hypothesis. This work is, to the</div><div>best of our knowledge, the first molecular dynamics study of RNA on ice</div>

Modified nucleotides may have enhanced early RNA catalysis

The modern version of the RNA World Hypothesis begins with activated ribonucleotides condensing (nonenzymatically) to make RNA molecules, some of which possess (perhaps slight) catalytic activity. We propose that noncanonical ribonucleotides, which would have been inevitable under prebiotic conditions, might decrease the RNA length required to have useful catalytic function by allowing short RNAs to possess a more versatile collection of folded motifs. We argue that modified versions of the standard bases, some with features that resemble cofactors, could have facilitated that first moment in which early RNA molecules with catalytic capability began their evolutionary path toward self-replication.

Molecular Dynamics simulations indicate solvation and stability of single-strand RNA at the air/ice interface, supporting a primordial RNA world on Ice

&lt;p&gt;Outstanding questions about the RNA world hypothesis for the emergence of life on Earth concern the stability and self-replication of prebiotic aqueous RNA. Recent experimental work has suggested that solid substrates and low temperatures could help resolve these issues. Here, we use classical molecular dynamics simulations to explore the possibility that the substrate is ice itself. We find that at -20 C, a quasi-liquid layer at the air/ice interface partially solvates a short (8-nucleotide) RNA strand such that the phosphate backbone anchors to the underlying crystalline ice structure though long-lived hydrogen bonds. The hydrophobic bases, meanwhile, are seen to migrate toward the outermost layer, exposed to air. Our simulations also reveal two key kinetic differences with respect to aqueous RNA. First, hydrogen bonds between solvent water molecules and phosphate diester moieties, believed to shield the RNA from hydrolysis, are much longer-lived for RNA on ice, compared to aqueous RNA at the same temperature. Second, contact between solvent water and ribose 2-OH&amp;#8217; groups, considered a precursor to nucleophilic attack by deprotonated 2-OH&amp;#8217; on the phosphate diester, is significantly less frequent for RNA on ice. Both differences point to lower susceptibility to hydrolysis of RNA on ice, and therefore increased opportunities for polymerization and self-copying compared to aqueous RNA. Moreover, exposure of hydrophobic bases at the air/ice interface offers opportunities for reaction that are not readily available to aqueous RNA (e.g., base-pairing reaction with free nucleotides diffusing across the air/ice interface). These findings thus offer the possibility of a role for an ancient RNA world on ice distinct from that considered in extant elaborations of the RNA world hypothesis. This work is, to the best of our knowledge, the first molecular dynamics study of RNA on ice.&lt;/p&gt;

Non-enzymatic primer extension with strand displacement

Non-enzymatic RNA self-replication is integral to the ‘RNA World’ hypothesis. Despite considerable progress in non-enzymatic template copying, true replication remains challenging due to the difficulty of separating the strands of the product duplex. Here, we report a prebiotically plausible solution to this problem in which short ‘invader’ oligonucleotides unwind an RNA duplex through a toehold/branch migration mechanism, allowing non-enzymatic primer extension on a template that was previously occupied by its complementary strand. Kinetic studies of single-step reactions suggest that following invader binding, branch migration results in a 2:3 partition of the template between open and closed states. Finally, we demonstrate continued primer extension with strand displacement by employing activated 3′-aminonucleotides, a more reactive proxy for ribonucleotides. Our study suggests that complete cycles of non-enzymatic replication of the primordial genetic material may have been catalyzed by short RNA oligonucleotides.