Fig. 1: Description of the non-enzymatic RNA polymerization and replication in an early Earth’s clay-water interface modeled by EarlyWorld.
From: Polymerization and replication of primordial RNA induced by clay-water interface dynamics
Top (A, B) sketch each natural compartment of the model and bottom (C, D) show example realizations of the evolution with time t of all the positions available in an oscillating clay environment. The bottom legend corresponds to the colors shown in (C, D). If not said otherwise, throughout this work we will use clays of length L = 200 positions, N = 1600 nts equally distributed between A, G, C, U types and initially placed in the aqueous phase, C ≡ G and A = U nucleobase complementarities, and simulation times \({t}_{\max }=2\times 1{0}^{4}\) time steps. Compartment I: Random polymerization occurs due to the catalytic action of clays in an interlayer of a clay grain, where complementary base pairing is not permitted due to steric hindrance. Only clay-nt interactions (of strength α) are permitted and ssRNA can be formed at the clay surface. Compartment II: The template replication of the original strand O occurs involving complementary base pairing; strand C (complementary to O) is formed, denatured from the template, released to the pool and adsorbed to the clay. In a next step, the replication of strand C yields strand R, whose sequence is equal to the original (R = O). Once the dsRNA molecule C-R is formed, its denaturation will release the ssRNA oligomer R, completing the RNA replication process. Other polymers Onew spuriously formed in comp.II can also be used as template (Cnew) and replicated (Rnew). In comp.II both clay-nt (of strength α) and nt-nt (of strength β) interactions are allowed, and ssRNA molecules can remain adsorbed to the clay (level 0), hybridize to their complementary strand to form dsRNA (level 1), or move to the aqueous phase (level 2). In this example, \(\alpha =0.8+0.5\sin (2\pi t/2500)\) and \(\beta =6+5.9\sin (2\pi t/2500)\).
