ArticleNucleic acids research2016
The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Prebiotically Plausible Synthesis of N-Cyanoimidazole for Phosphate Activation and Templated RNA Ligation.Journal of the American Chemical Society · 2026Article
- Abiotic synthesis of RNase-resistant phosphodiester and pyrophosphate-linked polymers via thermodynamically controlled wet-dry cycling.Scientific reports · 2026Article
- Article
- A quantitative model of enzyme-free copying of RNA with dimers.Nucleic acids research · 2025Article
- The Impact of Secondary Structure on the Base-Filling of N-Methoxy-1,3-Oxazinane (MOANA) and N-Methoxy-1,3-Oxazolidine Glycol Nucleic Acid (MOGNA) Oligonucleotides.Chembiochem : a European journal of chemical biology · 2025Article
- Constraints on the emergence of RNA through non-templated primer extension with mixtures of potentially prebiotic nucleotides.Nucleic acids research · 2024Article
- Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid-Phase and Template-Directed Chain Assembly.Chembiochem : a European journal of chemical biology · 2022Article
- Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor.Life (Basel, Switzerland) · 2022Article
- High Fidelity Enzyme-Free Primer Extension with an Ethynylpyridone Thymidine Analog.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- Single nucleotide translation without ribosomes.Nature chemistry · 2021Article
- Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension.Nucleic acids research · 2021Article
- The virtual circular genome model for primordial RNA replication.RNA (New York, N.Y.) · 2021Article
- Review
- 2'/3' Regioselectivity of Enzyme-Free Copying of RNA Detected by NMR.Chembiochem : a European journal of chemical biology · 2020Article
- Deep sequencing of non-enzymatic RNA primer extension.Nucleic acids research · 2020Article
- Enzyme-free ligation of dimers and trimers to RNA primers.Nucleic acids research · 2019Article
- Template-Directed Catalysis of a Multistep Reaction Pathway for Nonenzymatic RNA Primer Extension.Biochemistry · 2019Article
- Protocells and RNA Self-Replication.Cold Spring Harbor perspectives in biology · 2018Review
- Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA.Life (Basel, Switzerland) · 2018Review
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The template-directed incorporation of nucleotides at the terminus of a growing primer is the basis of the transmission of genetic information. Nature uses polymerases-catalyzed reactions, but enzyme-free versions exist that employ nucleotides with organic leaving groups. The leaving group affects yields, but it was not clear whether inefficient extensions are due to poor binding, low reactivity toward the primer, or rapid hydrolysis. We have measured the binding of a total of 15 different activated nucleotides to DNA or RNA sequences. Further, we determined rate constants for the chemical step of primer extension involving methylimidazolides or oxyazabenzotriazolides of deoxynucleotides or ribonucleotides. Binding constants range from 10 to >500 mM and rate constants from 0.1 to 370 M(-1) h(-1) For aminoterminal primers, a fast covalent step and slow hydrolysis are the main factors leading to high yields. For monomers with weakly pairing bases, the leaving group can improve binding significantly. A detailed mechanistic picture emerges that explains why some enzyme-free primer extensions occur in high yield, while others remain recalcitrant to copying without enzymatic catalysis. A combination of tight binding and rapid extension, coupled with slow hydrolysis induces efficient enzyme-free copying.
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