Nucleic acid phase separation and replication drive selection in prebiotic pools

Calaça Serrão, Adriana (2024): Nucleic acid phase separation and replication drive selection in prebiotic pools. Dissertation, LMU München: Fakultät für Physik

Abstract

Nucleic acids are considered to be early molecules owing to their dual ability to store information and catalyze reactions. The evolution of complex functional nucleic acids from a diverse pool of building blocks or short fragments necessitates the selective preference of certain sequences over others. The sequence space of nucleic acid pools with dozens or hundreds of bases is too vast to be fully explored. For this reason, it is believed that selection occurs as the pools become more complex, not only after attaining a sufficient length to support a ribozyme. Throughout the stages of nucleic acid elongation and copying, strands are subjected to various selection pressures, intrinsic to the replication or elongation mechanisms, or extrinsic, where certain sequences are better suited to survive in specific environments. In Chapter 1, selection for nucleic acids capable of phase separation was studied as the result of extrinsic selective pressures such as flux changes and dilution. Sequences capable of phase separation were enriched over cycles of supernatant removal by sedimenting at the bottom of the pore while other sequences were washed-out. These enriched sequences were the ones prone to forming network-like secondary structures. The wash-out and refeeding conditions mimic geological settings with varying fluxes such as bodies of water subjected to day-night cycles or tidal waves. Sequence pools with low compositional diversity (i.e. those that contained a binary alphabet - A / T or G / C ) did not exhibit phase separation. However, the introduction of a single mutation of the opposite alphabet restored this capacity, indicating a high sequence specificity of phase separation as a driving force for selection. In Chapter 2, the influence of replication on pools of short, biased oligomers was examined as an intrinsic factor. Random pools of short DNA strands, on average biased toward a specific nucleotide, underwent templated polymerization with Bst. While the overall pool compositional diversity increased at the nucleotide level due to the templated nature of the mechanism, remnants of the initial bias persisted at specific positions of the replicated strands. Initially unstructured pools developed patterns such as periodicity, enhancing replicability through increased intra- and inter-strand binding sites. In this case the overall pool composition also shifted to specific secondary structures, and therefore sequence motifs, due to the selective pressure exerted by the replication mechanism. In Chapter 3, a non-enzymatic RNA replication system employing 2′,3′-cyclic phosphates is described. This activation group, formed during RNA hydrolysis, nucleotide polymerization, and prebiotic phosphorylation, is readily available prebiotically. For the first time, templated RNA replication through ligation was achieved without the addition of organic catalysts. This system exhibited high sequence specificity, with a ligation fidelity exceeding 82%. Long sequences up to 100-mer were synthesized through consecutive ligation, paving the way for the creation of pools capable of hosting molecular evolution. Describing such a system represents the initial step in investigating the intrinsic influence of replication on a prebiotically plausible pool.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 530 Physik
• Fakultäten: Fakultät für Physik
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 8. Mai 2024
• 1. Bericht­erstatter:in: Braun, Dieter