Copying of RNA Sequences without Pre‐Activation
Open accessAbstract
Template‐directed incorporation of nucleotides at the terminus of a growing complementary strand is the basis of replication. For RNA, this process can occur in the absence of enzymes, if the ribonucleotides are first converted to an active species with a leaving group. Thus far, the activation required a separate chemical step, complicating prebiotically plausible scenarios. Here we show that a combination of a carbodiimide and an organocatalyst induces near‐quantitative incorporation of any of the four ribonucleotides. Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution. So, both de novo strand formation and sequence‐specific copying can occur without an artificial synthetic step.
Verified 2026-10-06 · 2 references not checked yet
AI snapshot
Written from the paper’s full text.
TL;DR
A carbodiimide plus an N-alkylated heterocycle enables in situ activation of free ribonucleotides, allowing enzyme-free primer extension on RNA templates without a separate pre-activation step. The same general condensation conditions also support untemplated oligomerization of ribonucleotides in aqueous solution.
Key findings
- With 0.8 M EDC and 1-ethylimidazole, primer extension by GMP reached 90% after 48 h at 20 °C; UMP incorporation reached 92% after 120 h at 0 °C. Near-quantitative incorporation was observed for all four ribonucleotides opposite their complementary bases in immobilized assays.
- Catalyst choice strongly affected copying: imidazole gave 2%, 2-methylimidazole 8%, 1-methyladenine 12%, and 1-ethylimidazole 32% extension after 24 h at pH 6.7. With 1-ethylimidazole, pH 7.5 gave 74% after 24 h and 90% after 48 h.
- Mg2+ was the fastest divalent metal tested: 70% extension after 1 d and 90% after 2 d; no extension occurred without a divalent metal, while Mn2+ gave 10% and Ca2+ 25% after 24 h.
- In situ activation also produced oligomers: for AMP, >90% of monomer was converted after 7 d, and chains of up to at least nine AMP residues were discernible after 30 d at 0 °C. For CMP, ≥25% monomer remained, and for UMP, ≥40% was unreacted after 7 d; GMP peaks were too broad for unambiguous assignment.
Methods
- Primer extension assays used RNA template–primer duplexes, some immobilized on magnetic beads via hybridization, and were monitored by MALDI-TOF mass spectrometry.
- Reactions used a “general condensation buffer”: 0.8 M EDC, 0.15 M 1-ethylimidazole, 0.08 M MgCl2, 0.5 M HEPES, pH 7.5, typically at 0 °C or 20 °C over days.
- Oligomerization was tested by ion-exchange HPLC and MALDI MS for AMP, UMP, CMP, or GMP solutions after one week at 0 °C, with an AMP assay run for 30 d.
Limitations
- The paper states that the strand-formation study was exploratory, that GMP oligomerization peaks were too broad for unambiguous assignment, and that mixed-sequence formation from all four ribonucleotides is presented in Ref. 33 rather than this work.
- Evident from the text: copying is demonstrated mainly as single-nucleotide primer extension, often with a downstream tetramer or hairpin limiting chain growth, not full replication of arbitrary sequences.
- Evident from the text: the conditions require high reagent concentrations, long reaction times, and low temperatures; prebiotic relevance is inferred from carbodiimide/cyanamide chemistry but not directly demonstrated here.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
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Cites
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Claims the paper makes
0 of 12 cited sources checked · 0 supported · 0 flagged
- Findingown data
In the absence of a divalent metal ion, no primer extension was observed.
“In the absence of a divalent metal ion, no primer extension was observed.”
Quote in the paperSubstantial claim - Findingown data
The combination of a carbodiimide and an N-alkyl heterocycle as catalyst induces efficient copying reactions on RNA templates using unactivated, free ribonucleotides.
“Here we show that a combination of a carbodiimide and an N-alkyl heterocycle as catalyst induces efficient copying reactions on RNA templates using unactivated, free ribonucleotides.”
Quote in the paperSubstantial claim - Findingown data
In each of three other templates offering C, G, or U, near-quantitative primer extension was observed with the corresponding ribonucleotide.
“In each case near-quantitative primer extension was observed (Figure 3 b–d).”
Quote in the paperSubstantial claim - Findingcitation
The incorporation of AMP opposite U is less than one order of magnitude slower than similar reactions involving pre-activated forms of AMP.
“This is less than one order of magnitude slower than similar reactions involving pre-activated forms of AMP.15, 39”
Quote in the paperSubstantial claim0 of 2 sources checked - Findingown data
A pH screen gave an optimum of 7.5 for primer extension.
“A subsequent screen of pH values gave an optimum of 7.5.”
Quote in the paperNot a substantial claim
- Findingown data
In an assay with AMP run for 30 d at 0 °C, peaks for chains of up to at least nine AMP residues are discernable.
“Figure 4 shows results from an assay with AMP run for 30 d at 0 °C. Peaks for chains of up to at least nine AMP residues are discernable.”
Quote in the paperSubstantial claim - Findingcitation
With 1-methyladenine as catalyst, 12% primer extension was observed after 1 d at 20 °C.
“With 1-methyladenine as catalyst,37 12 % primer extension was observed after 1 d at 20 °C.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [37] Prabahar KJ Ferris JP J. Am. Chem. Soc 1997 119 4330 4337 11543599
Not checked in the free run.
- Findingown data
Incorporation of AMP opposite U occurred with a half-life of approximately 3 d.
“Kinetics showed that incorporation of AMP opposite U occurred with a half-life time of approximately 3 d.”
Quote in the paperSubstantial claim - Findingown data
Lowering temperature to 0 °C led to near-quantitative incorporation of UMP after 5 d in 0.5 m HEPES buffer.
“Lowering the temperature to 0 °C, conditions close to those of eutectic ice phases, led to near-quantitative incorporation of UMP after 5 d in 0.5 m HEPES buffer (Figure 2 c, last entry in Table 1).”
Quote in the paperSubstantial claim - Findingown data
The reactions were surprisingly well behaved, with little to no side products detectable by MALDI MS.
“Despite the high concentrations, which are reminiscent of what is found in eutectic ice phases,11 the reactions were surprisingly well behaved, with little to no side products detectable by MALDI MS.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [11] Monnard P-A Kanavarioti A Deamer DW J. Am. Chem. Soc 2003 125 13734 13740 14599212 source
Not checked in the free run.
- Findingown data
Adding imidazole or 2-methylimidazole led to 2% conversion after 24 h.
“Adding imidazole or 2-methylimidazole led to 2 % conversion after 24 h.”
Quote in the paperNot a substantial claim - Findingown data
When 1-ethylimidazole was used, the yield of extended primer was 32% after 24 h.
“When 1-ethylimidazole was used, the yield of extended primer was 32 % after 24 h (Table 1).”
Quote in the paperSubstantial claim - Findingown data
Oligomerization of ribonucleotides occurs in the absence of a mineral surface.
“Oligomerization of ribonucleotides occurs in the absence of a mineral surface.”
Quote in the paperSubstantial claim - Findingown data
The vast majority of ribonucleotide molecules in solution remain unactivated upon treatment with EDC.
“Since NMR monitoring indicated that the vast majority of ribonucleotide molecules in solution remain unactivated upon treatment with EDC, reactions were expected to be inefficient.”
Quote in the paperSubstantial claim - Findingown data
No extension of primer 2 by GMP was detectable with EDC alone, even in high-salt buffer containing 0.8 m EDC.
“Initially, no extension of primer 2 by GMP was detectable, even in high-salt buffer containing 0.8 m EDC, and our experimental work aimed at high-yielding reactions was unsuccessful, in agreement with the low yields reported in the early literature.”
Quote in the paperSubstantial claim0 of 2 sources checked - Findingown data
With a mixture of GMP and CMP, two consecutive high-yielding copying steps occurred on a hairpin template.
“With the same buffer and a mixture of GMP and CMP, two consecutive high-yielding copying steps occurred on a hairpin template that prevents uncontrolled further extension (Figure 2 b).”
Quote in the paperSubstantial claim - Findingown data
Only when an organocatalyst was used did detectable copying set in.
“Only when an organocatalyst was used did detectable copying set in.”
Quote in the paperSubstantial claim - Findingown data
A combination of a carbodiimide and an organocatalyst induces near-quantitative incorporation of any of the four ribonucleotides.
“Here we show that a combination of a carbodiimide and an organocatalyst induces near-quantitative incorporation of any of the four ribonucleotides.”
- Also stated in: § Abstract · plain
“In each case near-quantitative primer extension was observed (Figure 3 b–d).”
- Also stated in: § Abstract · plain
“we report that the combination of a carbodiimide and an N-alkylated heterocycle as the catalyst induces high-yielding genetic copying.”
Quote in the paperSubstantial claim - Also stated in: § Abstract · plain
- Findingnone given
The efficiency of the reaction strongly depends on the choice of the covalent catalyst.
“The efficiency of the reaction strongly depends on the choice of the covalent catalyst.”
Quote in the paperSubstantial claim - Findingown data
Upon in situ activation, adenosine monophosphate forms oligomers in aqueous solution.
“Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution.”
- Also stated in: § Abstract · boosted
“In mass spectra of copying assays with AMP as the monomer, strong peaks for oligoadenylates were observed.”
Quote in the paperSubstantial claim - Also stated in: § Abstract · boosted
- Interpretationown data
Enzyme-free copying of RNA does not require pre-activation.
“This confirmed that enzyme-free copying of RNA does not require pre-activation.”
Quote in the paperSubstantial claim - Premisecitation
Free ribonucleotides act as competitive inhibitors of enzyme-free primer extension, blocking the extension site.
“These results are understandable because free ribonucleotides were shown to act as inhibitors of enzyme-free primer extension.”
- Also stated in: § Abstract · boosted
“The unactivated ribonucleotide was known to act as a competitive inhibitor to primer extension, blocking the extension site.”
Quote in the paperSubstantial claim0 of 2 sources checked - Also stated in: § Abstract · boosted
- Premisecitation
GMP pairs more strongly than AMP, CMP, and UMP.
“This is the most favorable case among the four copying reactions, as GMP pairs more strongly than the other three ribonucleotides (AMP, CMP, and UMP).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [32] Kervio E Claasen B Steiner UE Richert C Nucleic Acids Res 2014 42 7409 7420 24875480 PMC4066754 source
Not checked in the free run.
- Interpretationown data
A positively charged imidazolium species, expected to form with 1-ethylimidazole, is apparently much more reactive than the well-established imidazolides.
“A positively charged imidazolium species, expected to form with 1-ethylimidazole, is apparently much more reactive than the well-established imidazolides.”
Quote in the paperSubstantial claim
- May combine two claims. 7
- The quote only partly states this claim. 1
May combine two claims.
Findingown dataOnly for AMP >90% of the monomer was converted after 7 d, whereas for CMP ≥25% remained, and ≥40% of UMP was unreacted after 7 d.
“Only for AMP >90 % of the monomer was converted after 7 d, whereas for CMP ≥25 % of the monomer remained, and ≥40 % of UMP was unreacted after 7 d.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataWith 80 mM Mg2+, 70% extension after 1 d and 90% conversion after 2 d were observed.
“The fastest reaction was observed with Mg2+, with 70 % extension after 1 d and 90 % conversion after 2 d (mass spectrum in Figure 2 a).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataBoth primer extension on preformed RNA strands and untemplated de novo oligomerization of ribonucleotides to RNA strands were observed.
“Both primer extension on preformed RNA strands and the untemplated de novo oligomerization of ribonucleotides to RNA strands were observed.”
Quote in the paperSubstantial claimThe quote only partly states this claim.
Findingown dataUMP incorporation opposite adenine was 75% after 2 d at 20 °C.
“When uridine 5′-monophosphate (UMP), the most weakly pairing nucleotide,32 was offered to a primer on a template with adenine as the first templating base, 75 % incorporation occurred after 2 d.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [32] Kervio E Claasen B Steiner UE Richert C Nucleic Acids Res 2014 42 7409 7420 24875480 PMC4066754 source
Not checked in the free run.
May combine two claims.
Interpretationown dataThe oligomerization takes place at a fast enough rate to provide strands that may act as templates or primers, but slowly enough not to dominate the reaction landscape, so that it still allows for sequence-selective copying steps.
“It takes place at a fast enough rate to provide strands that may act as templates or primers, but slowly enough not to dominate the reaction landscape, so that is still allows for sequence-selective copying steps.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationcitationThe fast oligomerization of AMP contrasts with the slow primer extension on A-rich templates, suggesting a kinetic compensation.
“The fast oligomerization of AMP is an interesting contrast to the slow primer extension on A-rich templates,40, 41 the second step of replication scenarios with strand formation and subsequent copying, suggesting a kinetic compensation.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [40] Hill AR Orgel LE Wu T Origins Life Evol. Biospheres 1993 23 285 290 8115162
Not checked in the free run.
- cites [41] Kervio E Hochgesand A Steiner UE Richert C Proc. Natl. Acad. Sci. USA 2010 107 12074 12079 20554916 PMC2901432
Not checked in the free run.
May combine two claims.
Interpretationown dataBoth de novo strand formation and sequence-specific copying can occur without an artificial synthetic step.
“So, both de novo strand formation and sequence-specific copying can occur without an artificial synthetic step.”
- Also stated in: § Abstract · boosted
“This shows for the first time that genetic copying can occur without the synthetic step of pre-activation of the ribonucleotide.”
Quote in the paperSubstantial claim- Rests on an assumption: 1-ethylimidazole (or an N-alkyl heterocycle) was available under prebiotic conditions.
- Rests on an assumption: The high concentrations of EDC and ribonucleotides used are prebiotically plausible.
- Rests on an assumption: The optimized reaction conditions (0.5 M HEPES, 0.08 M MgCl2, pH 7.5) are representative of prebiotic environments.
- The authors state this as an assumption: Cyanamide is formed under prebiotic conditions.
- Also stated in: § Abstract · boosted
May combine two claims.
Interpretationown dataGeneral condensation conditions induce both high-yielding copying reactions and untemplated de novo formation of RNA strands.
“Taken together, our results confirm that “general condensation conditions” induce both high-yielding copying reactions and the untemplated de novo formation of RNA strands.”
Quote in the paperSubstantial claim- Rests on an assumption: 1-ethylimidazole (or an N-alkyl heterocycle) was available under prebiotic conditions.
- Rests on an assumption: The high concentrations of EDC and ribonucleotides used are prebiotically plausible.
- Rests on an assumption: The optimized reaction conditions (0.5 M HEPES, 0.08 M MgCl2, pH 7.5) are representative of prebiotic environments.
- The authors state this as an assumption: Cyanamide is formed under prebiotic conditions.
The paper relies on this without support.
1-ethylimidazole (or an N-alkyl heterocycle) was available under prebiotic conditions.
“Here we show that a combination of a carbodiimide and an N-alkyl heterocycle as catalyst induces efficient copying reactions on RNA templates using unactivated, free ribonucleotides.”
“The buffer thus optimized was dubbed “general condensation buffer” (0.8 m EDC, 0.15 m 1-ethylimidazole, 0.08 m MgCl2, 0.5 m HEPES, pH 7.5) and was used in all subsequent assays.”
The paper relies on this without support.
The high concentrations of EDC and ribonucleotides used are prebiotically plausible.
“High concentrations are characteristic of eutectic ice phases, and the beneficial effect of low temperatures for copying was known.”
“Despite the high concentrations, which are reminiscent of what is found in eutectic ice phases,11 the reactions were surprisingly well behaved, with little to no side products detectable by MALDI MS.”
The paper relies on this without support.
The optimized reaction conditions (0.5 M HEPES, 0.08 M MgCl2, pH 7.5) are representative of prebiotic environments.
“The buffer thus optimized was dubbed “general condensation buffer” (0.8 m EDC, 0.15 m 1-ethylimidazole, 0.08 m MgCl2, 0.5 m HEPES, pH 7.5) and was used in all subsequent assays.”
The authors state this as an assumption.
Cyanamide is formed under prebiotic conditions.
“Carbodiimide is a tautomer of cyanamide, a compound formed under presumed prebiotic conditions.22–24”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Nucleoside 5'-phosphate reacts first with EDC to form a reactive isourea intermediate, then displacement by NEI yields NEI-activated monomers that can react with the primer.
“The nucleoside 5 ′ -phosphate reacts first with EDC to form a reactive isourea intermediate, then displacement by NEI yields NEI-activated monomers that can then react with the primer”
From Protocells and RNA Self-Replication (2018) · cites this paper as Jauker et al. 2015
The paper reports primer extension using nucleoside 5′-monophosphates, EDC, and 1-ethylimidazole (Experimental Section, page unavailable). Its conclusion says a reactive imidazolium species is *expected* to form, but our copy does not describe an isourea intermediate or establish the claimed sequence of displacement and reaction with the primer. The claim presents that proposed mechanism as established. (LLM, conf=0.86)
Experimental — accuracy not yet measuredChemistry that would reactivate hydrolyzed substrates, such as EDC and an N-alkyl imidazole, could lead to a high ligation yield.
“This suggests that chemistry that would reactivate hydrolyzed substrates, such as the combination of EDC and an N-alkyl imidazole explored by the Richert laboratory (Jauker et al. 2015), could lead to a high ligation yield.”
From Protocells and RNA Self-Replication (2018) · cites this paper as Jauker et al. 2015
Binding of an unactivated AGC trimer downstream of an activated G monomer conferred only a modest increase in the rate of addition of the G monomer to the primer.
“The binding of an unactivated AGC trimer, with either a 5′ hydroxyl or a 5′ phosphate, downstream of an activated G monomer conferred only a modest increase in the rate of addition of the G monomer to the primer (Figure 1c–f, reactions 4 and 5), consistent with previous reports of unactivated downstream ‘helper’ oligonucleotides (Deck et al., 2011; Jauker et al., 2015; Kervio et al., 2010).”
From Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides (2016) · cites this paper as Jauker et al., 2015
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Listed template bases omit the base needed for UMP copying
MinorThe three other templates are said to offer C, G, or U, yet the corresponding reactions include UMP. Elsewhere the paper identifies adenine-not any of those three bases-as the template base for UMP incorporation.
“primer 7 was hybridized to three other templates, each offering a different template base (C, G, or U). The resulting primer–template duplexes were allowed to react with the corresponding ribonucleotide (AMP, CMP, GMP or UMP).”
“When uridine 5′-monophosphate (UMP), the most weakly pairing nucleotide,32 was offered to a primer on a template with adenine as the first templating base, 75 % incorporation occurred after 2 d.”
2-Methylimidazole conversion disagrees with Table 1
MinorThe text says both imidazole and 2-methylimidazole gave 2% conversion after 24 hours, but Table 1 reports 8% for 2-methylimidazole under the listed conditions.
“Adding imidazole or 2-methylimidazole led to 2 % conversion after 24 h.”
“| 1, 2 | G | 2-MeIm | A | 6.7 | 20 | 24 | 8 |”
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- M. Jauker H. Griesser C. Richert Angew. Chem. Int. Ed.2015 DOI:10.1002/anie.201506593;Angew. Chem.2015 DOI:10.1002/ange.201506593. · DOI
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- Authors
- Jauker, M., Griesser, H., & Richert, C.
- Affiliations
- University of Stuttgart (DE)
- Corresponding author
- Richert, Clemens
- ORCID
- Richert, Clemens
- Venue
- Angewandte Chemie International Edition
- Publisher
- Wiley
- Published
- 2015-10-05
- Volume
- 54
- Issue
- 48
- Pages
- 14559-14563
- ISSN
- 1433-7851 (ISSN-L)
- 1521-3773
- PMC
- PMC4678514
- OpenAlex
- W1819591220
- Cited by
- 72
- References
- 47
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 8 · 2023: 5 · 2022: 9 · 2021: 5 · 2020: 9 · 2019: 7 · 2018: 8 · 2017: 8 · 2016: 7 · 2015: 1
- FWCI
- 4.55
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Angewandte Chemie International Edition (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Funded Access
- DFG (RI 1063/8-2)
- EU
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- prebiotic chemistry, carbodiimides, organocatalysis, adenosine monophosphate
- MeSH terms
- Adenosine Monophosphate, RNA, Sequence Analysis, RNA
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