Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor

Abstract

The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium `RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.

Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization

“…Even phosphorylated threonine oligopeptides can be produced directly under the catalysis of DIPP-Thr as shown in the right route of figure 4 [50]. Furthermore, many prior investigations have indicated that phosphorylation of prebiotic substrates in aqueous settings occurs more frequently in incompatible and unique environments, resulting in the formation of matching oligomers or higher order structures [95][96][97][98][99][100][101][102]. The oligomerization of nucleotides was first attempted by heating 2 0 /3 0 -NMP at 160°C, which resulted in a complicated mixture of very short oligonucleotides [103].…”

Template-based information transfer in chemically fueled dynamic combinatorial librar-ies

“…Unlike in stochastic simulations of combinatorial libraries 60,61 , where different compounds can appear or disappear dynamically, in chemical rate equations, all (relevant) chemical compounds need to be considered at each timestep, which is memory intensive. However, in the present context, the chemical rate equation approach has technical advantages: (i) A timescale separation between (de)hybridization and polymerization can be considered by solving a set of algebraic equations at each time step.…”

The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity

“…There have been significant efforts to analyze the efficacy of both these scenarios. The temperature gradient of submarine hydrothermal vents have been shown to be useful for RNA polymerization reactions in creating long RNA molecules [ 36 , 37 , 38 , 39 ]. Normally, in aqueous solutions, the average length of polymers depends on the polymerization ( ) and hydrolysis rates ( ) as [ 40 ].…”