AFM Images of Viroid-Sized Rings That Self-Assemble from Mononucleotides through Wet–Dry Cycling: Implications for the Origin of Life (original) (raw)
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It is possible that early life relied on RNA polymers that served as ribozyme-like catalysts and store genetic information1,2. The source of such polymers is uncertain, but previous investigations reported that wet-dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers3. The aim of the study reported here was to visualize the products by atomic force microscopy. In addition to globular oligomers, ring-like structures ranging from 10-200 nm in diameter with an average around 30-40 nm were abundant, particularly when nucleotides capable of base pairing were present. The thickness of the rings was consistent with single stranded products, but some had thicknesses indicating base pair stacking. Others had more complex structures in the form of short polymer attachments and pairing of rings. These observations suggest the possibility that template-directed synthesis may occur during wet-dry cycling follow...
Visualizing RNA polymers produced by hot wet-dry cycling
2022
It is possible that the transition from abiotic systems to life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet–dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers and polymers. The aim of the study reported here was to verify this claim and visualize the products prepared from solutions composed of single mononucleotides and 1:1 mixture of two mononucleotides. Therefore, we designed experiments that allowed comparisons of all such mixtures representing six combinations of the four mononucleotides of RNA. We observed irregular stringy patches and crystal strands when wet-dry cycling was performed at room temperature (20 o C). However, when the same solutions were exposed to wet–dry cycles at 80 o C, we observed what appeared to be true polymers. Their thickness...
Life
We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3′–C5′ hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet–dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bon...
RNA auto-polymerisation from 2’,3’-cyclic nucleotides at air-water interfaces
2022
For the emergence of life, the abiotic synthesis of RNA from its monomers is a central challenge. We found alkaline drying conditions in bulk and at heated air-water interfaces where 2 ́,3 ́-cyclic nucleotides reacted to form copolymers up to 10-mers. The polymerisation proceeded at a pH range of 7-12, temperatures between 40-80 °C and was enhanced by K+ ions. Among the canonical nucleotides, cGMP polymerised most efficiently. Our study suggests a polymerisation mechanism where cGMP polymerises first to form a polymorphic scaffold into which the other relatively unreactive nucleotides copolymerise. The 2 ́,3 ́-cyclic monomers are often products in prebiotic phosphorylation, nucleotide syntheses and recyclable intermediates of RNA hydrolyses. The plausible abiotic availability and the simple dry polymerisation conditions, combined with hydrolytic recycling offers an appealing minimal entry point for RNA-based molecular evolution on early Earth.
Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers
Scientific reports, 2016
RNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. However, in the absence of enzymes and metabolism there has been no obvious way for RNA-like molecules to be produced and then encapsulated in cellular compartments. We investigated 5'-adenosine monophosphate (AMP) and 5'-uridine monophosphate (UMP) molecules confined in multi-lamellar phospholipid bilayers, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay, previously proposed to promote polymerization. X-ray diffraction was used to determine whether such conditions imposed a degree of order on the nucleotides. Two nucleotide signals were observed in all matrices, one corresponding to a nearest neighbour distance of 4.6 Å attributed to nucleotides that form a disordered, glassy structure. A second, smaller distance of 3.4 Å agrees well with the distance between stacked...