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Updated: Sep 1, 2025

Chemical Triphosphorylation of Oligonucleotides
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A Ribonucleotide ↔ Phosphoramidate Reaction Network Optimized by Computer-Aided Design.

Andreas Englert1, Julian F Vogel1, Tim Bergner2

  • 1Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.

Journal of the American Chemical Society
|August 11, 2022
PubMed
Summary
This summary is machine-generated.

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This study details a new out-of-equilibrium chemical system using ribonucleotides to form phosphoramidates, relevant for origin-of-life research. A catalyst (1-ethylimidazole) significantly impacts hydrolysis rates, enabling transient self-assemblies.

Area of Science:

  • Chemical kinetics
  • Systems chemistry
  • Origin of life studies

Background:

  • Out-of-equilibrium chemical systems are increasingly studied.
  • Dissipative reaction networks, driven by chemical fuels, are rare, especially non-enzymatic ones.
  • Existing non-enzymatic examples often rely on carbodiimide chemistry.

Purpose of the Study:

  • To establish a novel dissipative reaction network using natural ribonucleotides.
  • To investigate the formation of phosphoramidates and their subsequent hydrolysis.
  • To explore the potential for generating self-assembled structures relevant to prebiotic chemistry.

Main Methods:

  • Utilized a chemical fuel to drive phosphoramidate formation from ribonucleotides (e.g., GMP, AMP).
  • Employed a mild phosphoramidate hydrolysis as the backward reaction.

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  • Applied Design of Experiments (DoE) for network optimization and understanding.
  • Characterized transient self-assemblies using dynamic light scattering (DLS), confocal microscopy (CLSM), and cryogenic transmission electron microscopy (cryo-TEM).

    • Main Results:

    • Successfully constructed a dissipative reaction network based on phosphoramidate chemistry.
    • Identified 1-ethylimidazole (EtIm) as a potent nucleophilic catalyst for hydrolysis, mimicking enzyme activity.
    • Observed the formation of transient self-assemblies from prebiotically plausible building blocks.

    Conclusions:

    • The developed reaction cycle offers a new non-enzymatic model for out-of-equilibrium chemistry.
    • The catalytic effect of EtIm provides insights into biochemical mechanisms.
    • The formation of self-assemblies from simple precursors has implications for understanding the origin of life.