In Situ Imidazole Activation of Ribonucleotides for Abiotic RNA Oligomerization Reactions

Abstract

The hypothesis that RNA played a significant role in the origin of life requires effective and efficient abiotic pathways to produce RNA oligomers. The most successful abiotic oligomerization reactions to date have utilized high-energy, modified, or pre-activated ribonucleotides to generate strands of RNA up to 50-mers in length. In spite of their success, these modifications and pre-activation reactions significantly alter the ribonucleotides in ways that are highly unlikely to have occurred on a prebiotic Earth. This research seeks to address this problem by exploring an aqueous based method for activating the canonical ribonucleotides in situ using 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and imidazole. The reactions were run with and without a montmorillonite clay catalyst and compared to reactions that used ribonucleotides that were pre-activated with imidazole. The effects of pH and ribonucleotide concentration were also investigated. The results demonstrate the ability of in situ activation of ribonucleotides to generate linear RNA oligomers in solution, providing an alternative route to produce RNA for use in prebiotic Earth scenarios.

Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

“…The instrument used to analyze the polymerization products of the in situ experiments provided better resolution than the instruments used in the other experiments and improved our ability to distinguish AMP from IMP, and CMP from UMP. The MALDI MS spectra of the in situ activation reaction products generally were more complex than those for the reactions of preactivated ImpX due to greater contributions from reaction side products, as previously reported (Burcar et al 2015). These side products are likely due to the presence of reagents and metals in the in situ reactions that would have been removed from the pre-activated ImpX prior to use.…”

“…To more closely approximate early Earth conditions in which nucleotides would be activated in situ in an aqueous environment rather than pre-activated in dry, organic solvents, an in situ method of imidazole activation previously developed in our group (Burcar et al 2015) was employed. The reaction scheme is shown in Figure 8.…”

“…Next, we investigated polymerization in mixtures of multiple, pre-activated nucleotides. Finally, polymerization reactions were performed using in situ imidazole activation in the polymerization reaction itself (Burcar et al 2015), thereby avoiding the need for preactivation of the nucleotides via organic (non-aqueous) synthesis. The in situ approach is a more realistic scenario than the use of nucleotides preactivated via organic synthesis in non-aqueous solvents.…”

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World

“…Experiments that show RNA polymerization have been carried out using clay catalysts [12–14] and using wetting and drying cycles in the presence of lipid bilayers or ammonium chloride salt [15–18]. Wet-dry cycling seems to promote polymerization because polymer bond formation becomes thermodynamically favourable in the dry phase but continued polymer growth is limited by restricted diffusion.…”

Controlled supramolecular structure of guanosine monophosphate in the interlayer space of layered double hydroxide

“…In that literature, peptidic condensation of amino acids was determined to favor heteropeptide rather than homopeptide. Besides polymerization of amino acids, it was reported that abiotic oligomerization of RNA nucleotides was catalyzed by montmorillonite clay [7]. In the presence of clay, the length of polymerized RNA oligonucleotides was three times longer than without clay.…”