4 research outputs found
Selection of prebiotic oligonucleotides by cyclic phase separation
The emergence of functional oligonucleotides on early Earth required a
molecular selection mechanism to screen for specific sequences with prebiotic
functions. Cyclic processes such as daily temperature oscillations were
ubiquitous in this environment and could trigger oligonucleotide phase
separation. Here, we propose sequence selection based on phase separation
cycles realized through sedimentation in a system subjected to the feeding of
oligonucleotides. Using theory and experiments with DNA, we show
sequence-specific enrichment in the sedimented dense phase, in particular of
short 22-mer DNA sequences. The underlying mechanism selects for
complementarity, as it enriches sequences that tightly interact in the
condensed phase through base-pairing. Our mechanism also enables initially
weakly biased pools to enhance their sequence bias or to replace the most
abundant sequences as the cycles progress. Our findings provide an example of a
selection mechanism that may have eased screening for the first auto-catalytic
self-replicating oligonucleotides
High-Fidelity Templated Ligation of RNA via 2′,3′-cyclic Phosphate
The templated ligation of oligonucleotides offers a mode of replication in an RNA world. The 2′,3′-cyclic phosphate (>P) is a prebiotically available activation group for RNA and the product of backbone hydrolysis. Using gel electrophoresis and liquid chromatography, we found that the templated ligation of RNA with >P activation proceeds in alkaline (pH 9-11) low-salt aqueous solutions with 1 mM MgCl2 in temperatures ranging from 20 to 25 °C within a few days. Under the optimum conditions of pH 10 and 5 °C, the ligation yielded 40% after 7 days. No additional catalysts were required. In contrast to previous reports, we found an equimolar mixture of 2′-5′ and 3′-5′ linked oligomers in the used conditions. We probed the nucleotide specificity at the ligation site and found that one mutation reduced the ligation yield by 82-92%. We extrapolated these results to a per-nucleotide replication fidelity of 95-98% when ligating 4- to 6-mers. With splinted oligomers, five ligations created a 96 mer strand, demonstrating a possible assembly pathway for long ribozymes. With the low salt requirements, strand separation will be compatible with the ligation conditions using non-equilibrium settings. The findings suggest that templated ligation mediated by 2′,3′-cyclic phosphate in alkaline conditions offer a slow, but precise replication and elongation reaction for RNA on early Earth
Heated gas bubbles enrich, crystallize, dry, phosphorylate and encapsulate prebiotic molecules
Non-equilibrium conditions must have been crucial for the assembly of the first informational polymers of early life, by supporting their formation and continuous enrichment in a long-lasting environment. Here, we explore how gas bubbles in water subjected to a thermal gradient, a likely scenario within crustal mafic rocks on the early Earth, drive a complex, continuous enrichment of prebiotic molecules. RNA precursors, monomers, active ribozymes, oligonucleotides and lipids are shown to (1) cycle between dry and wet states, enabling the central step of RNA phosphorylation, (2) accumulate at the gas-water interface to drastically increase ribozymatic activity, (3) condense into hydrogels, (4) form pure crystals and (5) encapsulate into protecting vesicle aggregates that subsequently undergo fission. These effects occur within less than 30 min. The findings unite, in one location, the physical conditions that were crucial for the chemical emergence of biopolymers. They suggest that heated microbubbles could have hosted the first cycles of molecular evolution