Virtual Circular Genome Model for Prebiotically Plausible Nonenzymatic RNA Replication

Abstract

Nonenzymatic RNA replication is thought to have been an essential step on the path to the emergence of the first ribozymes during the origin of life. However, current nonenzymatic RNA replication models are limited by the extent and fidelity of primer extension chemistry, and the difficulty of copying the strands of the product duplex. Here we discuss the virtual circular genome (VCG) model, which is based on a collection of short oligonucleotides that map onto both strands of one or more virtual circular sequences. Replication is driven by annealing of the oligonucleotides to allow for templated primer extension or ligation, followed by rearrangement to allow additional oligonucleotide elongation. Every oligonucleotide in the system can act as a primer, template, or downstream helper. Therefore, the genomic replication process is distributed across the population. Over multiple generations, this model can be viewed as a flow of material from shorter to longer oligonucleotides that cover the genome. We have monitored the fate of individual primers in the pool of oligonucleotides, and have investigated factors such as oligo length, concentration, temperature, and metal catalyst on the primer extension yield. We propose several strategies that may lead to fast and accurate primer extension in the VCG model, and which may eventually enable cycles of genome replication and the evolution of ribozymes within replicating protocells.