Potentially Prebiotic Synthesis of Aminoacyl-RNA via a Bridging Phosphoramidate-Ester Intermediate

Abstract

Translation according to the genetic code is made possible by selectivity both in aminoacylation of tRNA and in anticodon/codon recognition. In extant biology, tRNAs are selectively aminoacylated by enzymes using high-energy intermediates, but how this might have been achieved prior to the advent of protein synthesis has been a largely unanswered question in prebiotic chemistry. We have now elucidated a novel, prebiotically plausible stereoselective aminoacyl-RNA synthesis, which starts from RNA-amino acid phosphoramidates and proceeds via phosphoramidate-ester intermediates that subsequently undergo conversion to aminoacyl-esters by mild acid hydrolysis. The chemistry avoids the intermediacy of high-energy mixed carboxy-phosphate anhydrides and is greatly favored under eutectic conditions, which also potentially allow for the requisite pH fluctuation through the variable solubility of CO 2 in solid/liquid water.

A Ribonucleotide ↔ Phosphoramidate Reaction Network Optimized by Computer-Aided Design

“…Due to the simplicity of all building blocks (except perhaps the fuel), such a system may have prebiotic relevance. 28,47,49 Furthermore, the use of an alkylamine rather than benzylamine demonstrates the relatively broad scope of the approach. Using alkylamines required only moderate adjustment of the reaction conditions, probably due to differences in pK a .…”

“…Having optimized the dissipative reaction cycle, we wondered whether the combination of an alkylamine with a monophosphate could give rise to the transient self-assembly of compartments (Figure A). Due to the simplicity of all building blocks (except perhaps the fuel), such a system may have prebiotic relevance. ,, Furthermore, the use of an alkylamine rather than benzylamine demonstrates the relatively broad scope of the approach. Using alkylamines required only moderate adjustment of the reaction conditions, probably due to differences in p K a .…”

“…Arguably, the most popular chemical fuels in artificial dissipative networks, especially in those that do not require enzyme catalysis, are carbodiimides such as 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) . Although the prebiotic plausibility of carbodiimide fuels is questionable, − EDC is valuable as a model reagent because of its water solubility, slow background reaction with water, and its exceptionally well-understood reaction profile . For these reasons, EDC has been successfully used in a large number of recent studies on transient behavior.…”

“…For example, efficient non-enzymatic primer extension of 3′-NP DNA , and template-directed synthesis of 3N′-5P′-RNA have been reported (self-replication). Moreover, it was shown that prebiotically plausible stereoselective aminoacyl-RNA synthesis and even ribosome-like translation (metabolism) contain phosphoramidate intermediates. Both the formation − and the hydrolysis − as well as the self-assembly , of phosphoramidates have been studied individually.…”

Exchange, catalysis and amplification of encapsulated RNA driven by periodic temperature changes

“…Frozen conditions have also been shown to promote both nucleotide activation and nonenzymatic templated copying of RNA 30 , as well as host more complex ribozyme reactions that increase genotype / phenotype complexity of the starting RNA pools [31][32][33] . Even a plausible pathway for the synthesis of peptide-RNA is promoted by water-ice formation and the pH change that accompanies it 34 .…”