Complete RNA replication cycles in a Hadean microcompartment

Abstract

The replication of nucleic acids is a prerequisite for the survival and evolution of living systems. Before the advent of protein synthesis, genetic information was most likely stored on and replicated by RNA. However, experimental systems for sustained RNA-dependent RNA-replication are difficult to realise due to the high thermodynamic stability of duplex products and the low chemical stability of catalytic polynucleotides. Using a derivative of a group I intron as a model for an RNA replicase, we show that heated air-water interfaces exposed to a plausible CO2-rich atmosphere drive complete cycles of plus and minus strand replication. The reaction is driven by autonomous oscillations in salt concentrations and pH that transiently destabilise RNA duplexes. Newly synthesised strands can dissociate from their templates and adopt catalytically active conformations. Our results suggest that an abundant Hadean microenvironment may have promoted the replication of RNAs while maintaining the activity of the synthesised ribozymes.

Constrained dynamics of oligonucleotides in the phase-separated droplets

“…in phase-separated droplets. The proposition of such droplets as model “protocell” by Oparin and Haldane (30, 31) has sparked a number of experimental works involving functional DNA/RNA and phase-separated droplets (5–9). However, there are limited studies examining the internal dynamics of oligonucleotides inside these droplets.…”

High-Fidelity Templated Ligation of RNA via 2′,3′-cyclic Phosphate

“…Thus, one can envision a ligation chain reaction triggered by thermal cycling of the reaction mixture similar to Edeleva et al, with the benefit of not generating deleterious side-products by EDC. [21] Additionally, a ligating ribozyme such as sunY [56,57] having typically high (50 mM) magnesium requirements, has been shown to ligate in the low (5 mM) Mg 2+ solutions under thermal non-equilibrium conditions of an air-water interface which offers continuous feeding [26] . This suggests that such scenarios could provide a niche where the ligation reactions by 2′,3′-cyclic phosphate could evolve towards a ribozymatic replicator.…”

“…Over the years, non-enzymatic templated ligation has been shown for RNA, DNA and XNA [13][14][15] via chemical activations like imidazolides and its analogues [16][17][18][19][20] , carbodiimides [21][22][23] , pyrophosphate [19,20,24] . Without these chemical activations, the formation of 40-200nt long ligating ribozymes seems impossible [25][26][27] . However, many of these 60 reactions require multiple synthesis steps to generate the required activated molecules such as phosphorimidazolides.…”

Multispecies autocatalytic RNA reaction networks in coacervates

“…Some of the foundational work involves demonstrations of RNA exchange between a coacervate and its environment Jia et al (2014) and the catalytic activity of RNA cleavage and template-based polymerization in coacervates or ATPS (aqueous two-phase systems) Drobot et al (2018); Poudyal et al (2019); Strulson et al (2012). Furthermore, several recent studies report some critical steps towards the construction of an evolvable coacervate-based protocell, e.g ., catalytic assembly of longer RNA in condensates Le Vay et al (2021), RNA reproduction via ligase activity Iglesias-Artola et al (2022); Salditt et al; Salibi et al. However, the (auto-)catalytic assembly of longer (larger) molecules from constituent fragments, the creation of reaction networks and achieving self-reproduction remain explored.…”