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Cited by 54DNA and Nucleic Acid ChemistryRNA and protein synthesis mechanismsOrigins and Evolution of Life

The strength of the template effect attracting nucleotides to naked DNA

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Kervio, E., Claasen, B., Steiner, U. E., Richert, C.·2014·Nucleic Acids Research
DOI 10.1093/nar/gku314PMC PMC4066754
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Abstract

The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template-primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd's range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.

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  • With single nucleotides, the dissociation constant (>2 mM) requires high concentrations of activated monomers in primer extension reactions.

    “With single nucleotides, the dissociation constant (>2 mM) requires high concentrations of activated monomers in the primer extension reactions.21”

    From Sequencing of <scp>d</scp>/<scp>l</scp>-DNA and XNA by Templated-Synthesis (2025) · cites this paper as [21]

  • 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.”

    From Copying of RNA Sequences without Pre‐Activation (2015) · cites this paper as [32]

  • 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).”

    From Copying of RNA Sequences without Pre‐Activation (2015) · cites this paper as [32]

  • UMP 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.”

    From Copying of RNA Sequences without Pre‐Activation (2015) · cites this paper as [32]

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Authors
Kervio, E., Claasen, B., Steiner, U. E., & Richert, C.
Affiliations
  • University of Stuttgart (DE)
  • University of Konstanz (DE)
Corresponding author
Richert, C.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2014-05-29
Volume
42
Issue
11
Pages
7409-7420
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gku314
PMC
PMC4066754
OpenAlex
W2114044732
Cited by
54
References
9
Citations by year
2026: 1 · 2025: 2 · 2024: 4 · 2023: 6 · 2022: 5 · 2021: 4 · 2020: 4 · 2019: 4 · 2018: 2 · 2017: 7 · 2016: 5 · 2015: 7 · 2014: 3
FWCI
3.15
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • KOPS (University of Konstanz) (submittedVersion, cc-by)
Funders
Deutsche Forschungsgemeinschaft (RI 1063/8-2)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
Keywords
template effect, dissociation constant, Watson-Crick base pairing, origin of life, genetic information transfer, DNA hydrolysis
MeSH terms
Deoxyribonucleotides, DNA, Templates, Genetic, DNA Primers

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