Groundbreaking Discovery Reveals Chemical Pathway for RNA Aminoacylation and Peptidyl-RNA Formation in Water
In a remarkable advance towards understanding the molecular origins of life, researchers have unveiled a novel chemical pathway that facilitates the aminoacylation of RNA and subsequent peptidyl-RNA synthesis in purely aqueous environments. This unprecedented work elegantly demonstrates how thioesters and thioacids, distinct yet complementary sulfur-containing compounds, enable stepwise, selective reactions under mild, neutral conditions that mimic plausible prebiotic scenarios.
The study centers on the delicate balance of reactivity between naturally occurring RNA 2′,3′-diols and aminoacyl-thiols, a class of biologically activated thioesters. By precisely tuning this interaction, the research team achieved efficient and highly selective aminoacylation of nucleosides in water, forming aminoacylated RNA under conditions that do not promote unwanted side reactions such as peptide bond formation. This selectivity arises from the orthogonal nature of thioester activation compared to the classical peptide bond-forming pathways, highlighting a crucial mechanistic divergence that facilitates biomimetic peptide synthesis orchestrated by nucleic acids.
To rigorously probe the specificity of these reactions, the team conducted incisive experiments investigating the interplay between aminoacyl-thiol species and RNA substrates. Remarkably, when the free amine functionality of aminoacyl-thiols was blocked via N-acetylation, no peptidyl-RNA formation was observed even after prolonged incubation, underscoring the essential role of the free amine in driving selective aminoacylation at the RNA diol position. Moreover, attempts to generate peptidyl-RNA directly from aminoacyl-thiols and RNA proved unsuccessful under neutral pH, despite the presence of an excess of reactive thioesters. These results collectively suggest the presence of a finely tuned chemical “switch” that governs whether peptide elongation proceeds or aminoacylation stops, a finding with profound implications for the stepwise chemical evolution of early life polymers.
Comparing these findings to existing peptide synthesis techniques further illuminates the unique nature of the thioester system. For instance, traditional methods employing highly activated carbodiimides such as EDC enable peptide bond formation through indiscriminate amine acylation in water. Contrarily, aminoacyl-thiols feature much weaker activation, preventing peptide formation despite the coexistence of free amines and reactive thioesters. This stark contrast points to the remarkable capacity of thioester chemistry to mediate selective RNA aminoacylation without unleashing uncontrolled peptide synthesis—a feature vital for the hypothesized evolution of RNA-templated peptide assembly.
Expanding on this insight, the researchers next explored the potential of peptide thioacids as alternative activation intermediates. These thioacids, accessible from thioesters through hydrogen sulfide treatment, exhibit a unique propensity to be selectively activated under mildly oxidizing conditions using ferricyanide, copper salts, or cyanoacetylene. When introduced to aminoacyl-RNA conjugates, these activated peptide thioacids efficiently and selectively catalyze the formation of peptidyl-RNA bonds, facilitating coupling reactions that preserve stereochemical integrity without side reactions on nucleoside hydroxyls or nucleobases.
Through careful ^1H NMR analysis, the team demonstrated near-quantitative conversion of aminoacyl-RNA intermediates to their peptidyl-RNA counterparts in water under neutral pH, highlighting the impressive functional orthogonality of thioester and thioacid chemistries. This dual activation strategy permits the controlled synthesis of peptidyl-RNAs in a single reaction vessel, an achievement that brings researchers a crucial step closer to realizing non-enzymatic, protecting-group-free peptide synthesis mediated by nucleic acids.
Importantly, the preservation of stereochemistry throughout this dual-step reaction sequence confirms the mechanistic finesse of the approach. Neither racemization of aminoacyl-thiols nor epimerization during peptide bond formation was observed, yielding homochiral peptidyl-RNAs. This exquisite chiral fidelity supports the notion that under prebiotic conditions, selectivity and stereochemical control could be intrinsically built into simple chemical networks reliant on sulfur-based activation.
The study further clarifies that the observed selectivity cannot be attributed to simple protonation effects at physiological pH. Instead, the distinct chemical properties of thioesters versus thioacids create the necessary orthogonality enabling sequential control over aminoacylation and peptide extension. In this way, thioesters prime the nucleoside diol for aminoacylation, while thioacids, after specific activation, promote ligation into peptidyl-RNA. Crucially, these complementary pathways coexist under identical aqueous conditions—demonstrating a plausible prebiotic blueprint for peptide-RNA coevolution.
One particularly striking part of the investigation was the execution of a true one-pot reaction where RNA, aminoacyl-thiols (thioesters), and peptide thioacids were combined in a carefully buffered aqueous solution. Over the course of incubation and addition of an oxidant, the reaction progressed from nucleoside aminoacylation directly to efficient peptidyl-RNA formation without isolation of intermediates. This operational simplicity marks a milestone for bottom-up synthetic approaches seeking to model early biopolymer chemistry and illuminates a versatile platform for synthetic biology applications.
The robustness and broad applicability of this method were further underlined by successful peptide ligations encompassing all 20 proteinogenic amino acids, tolerating diverse side chains without compromising yield or selectivity. Such broad chemical tolerance attests to the potential universality of thioester/thioacid-mediated RNA aminoacylation and peptidyl-RNA synthesis mechanisms in the context of primitive biochemical pathways.
Beyond the exciting prebiotic chemistry implications, these findings could transform our understanding of early ribonucleoprotein systems by providing concrete chemical evidence for RNA’s capacity to directly orchestrate peptide bond formation. This challenges traditional views that enzymes were strictly necessary for translational polymerization and opens avenues into exploring non-enzymatic peptide assembly routes guided by RNA scaffolds.
In summary, this pioneering research offers compelling evidence that nucleic acids and sulfur-based acylating agents can collaborate under mild, aqueous conditions to drive the sequential chemical transformations essential for fragmenting peptides tethered to RNA. Such chemistry not only advances our comprehension of molecular evolution but also inspires innovative strategies in synthetic biology, chemical synthesis, and nanotechnology by harnessing nature’s own elegant principles from its earliest stages.
Amidst the quest to unravel life’s origins, these chemical discoveries elucidate a plausible and elegant route bridging RNAs and peptides through tailored thioester and thioacid chemistries. The results pave the way for future explorations into macromolecular co-assembly, RNA-driven catalysis, and the ultimate genesis of the genetic code itself.
Subject of Research: Mechanistic investigation of RNA aminoacylation and peptide synthesis mediated by thioester and thioacid chemistry under aqueous, prebiotically relevant conditions.
Article Title: Thioester-mediated RNA aminoacylation and peptidyl-RNA synthesis in water.
Article References:
Singh, J., Thoma, B., Whitaker, D. et al. Thioester-mediated RNA aminoacylation and peptidyl-RNA synthesis in water. Nature 644, 933–944 (2025). https://doi.org/10.1038/s41586-025-09388-y
Image Credits: AI Generated
DOI: https://doi.org/10.1038/s41586-025-09388-y
Keywords: RNA aminoacylation, peptidyl-RNA synthesis, thioesters, thioacids, non-enzymatic peptide synthesis, prebiotic chemistry, biomimetic peptide ligation, molecular evolution, nucleic acid catalysis, chemical origins of life
