Variation in G-quadruplex sequence and topology differentially impacts human DNA polymerase fidelity
Open accessAbstract
G-quadruplexes (G4s), a type of non-B DNA, play important roles in a wide range of molecular processes, including replication, transcription, and translation. Genome integrity relies on efficient and accurate DNA synthesis, and is compromised by various stressors, to which non-B DNA structures such as G4s can be particularly vulnerable. However, the impact of G4 structures on DNA polymerase fidelity is largely unknown. Using an in vitro forward mutation assay, we investigated the fidelity of human DNA polymerases delta (δ4, four-subunit), eta (η), and kappa (κ) during synthesis of G4 motifs representing those in the human genome. The motifs differ in sequence, topology, and stability, features that may affect DNA polymerase errors. Polymerase error rate hierarchy (δ4 < κ < η) is largely maintained during G4 synthesis. Importantly, we observed unique polymerase error signatures during synthesis of VEGF G4 motifs, stable G4s which form parallel topologies. These statistically significant errors occurred within, immediately flanking, and encompassing the G4 motif. For pol δ4, the errors were deletions, insertions and complex errors within the G4 or encompassing the G4 motif and surrounding sequence. For pol η, the errors occurred in 3' sequences flanking the G4 motif. For pol κ, the errors were frameshift mutations within G-tracts of the G4. Because these error signatures were not observed during synthesis of an antiparallel G4 and, to a lesser extent, a hybrid G4, we suggest that G4 topology and/or stability could influence polymerase fidelity. Using in silico analyses, we show that most polymerase errors are predicted to have minimal effects on predicted G4 stability. Our results provide a unique view of G4s not previously elucidated, showing that G4 motif heterogeneity differentially influences polymerase fidelity within the motif and flanking sequences. Thus, our study advances the understanding of how DNA polymerase errors contribute to G4 mutagenesis.
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Error-prone polymerases might be engaged at slowed or stalled replication forks to ensure complete G4 replication, as specialized polymerases like eta, kappa, and Rev1 are essential for G4 stability, further increasing the density of localized genomic damages.
“Error-prone polymerases might be engaged at slowed or stalled replication forks to ensure complete G4 replication, as specialized polymerases like eta, kappa, and Rev1 are essential for G4 stability – further increasing the density of localized genomic damages (26,78–80).”
From G-quadruplex-mediated genomic instability drives SNVs in cancer (2024) · cites this paper as [78]
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Experimental — accuracy not yet measuredDNA polymerase errors during replication or repair processes at G4 loci contribute to elevated mutagenesis due to steric, G4 mediated inhibition.
“One possibility is that DNA polymerase errors during replication or repair processes at G4 loci contribute to elevated mutagenesis due to steric, G4 mediated inhibition (78).”
From G-quadruplex-mediated genomic instability drives SNVs in cancer (2024) · cites this paper as [78]
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“…initiation, and their deletion can impede this process (Valton et al. 2014; Prioleau 2017); (2) G4s can act as barriers to replication progression, leading to replication fork stalling (Stein et al. 2022) and contributing to genomic instability (Sun and Hurley 2010; Lormand et al. 2013).”
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“On the one hand, they can act as obstacles that stall replication forks (Stein et al. 2022), thereby fostering genomic instability (Sun and Hurley 2010; Lormand et al. 2013).”
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“These works have demonstrated unique polymerase error signatures during the synthesis of G4 motifs within, immediately flanking, and encompassing the G4 motif depended on the particular G4 topology and DNA polymerase (Stein et al., 2022).”
BackgroundBartosik, A. R., Bujnowska, M., Stovall, D. B., Ratan, A., & Wang, Y. (2026) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2026.2710103
“Aberrant G4 formation has been associated with higher nucleotide substitution rates (Guiblet et al. 2021a) and the enrichment of mutations linked to cancer, implicating G4s as contributors to somatic mutagenesis (Stein et al. 2022; Zhuk et al. 2024).”
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García-Ruano, D., Georges, M., Mohanty, S., Baaziz, R., Makova, K. D., Nikolski, M., & Chalopin, D. (2026) · bioRxiv · doi:10.64898/2026.04.14.718168
“Non-B DNA structures in the body of genes, including genes transcribing lncRNAs, affect replication [16,31], and transcription initiation and progression.”
Self-citationThermally activated irreversible homogenization of G-quadruplexes in an ALS/FTD-associated genePreprint
Ross, D., Lewis, O., McLean, O., Bhanot, S., Donahue, S., Baker, R., Dias, R., Eagerton, D., Mohanty, V., & Mohanty, B. (2025) · bioRxiv · doi:10.1101/2025.06.02.657482
“G4s can fold into different topologies, and it has been shown recently that these topologies can differentially impact fidelity of DNA synthesis (20).”
- Authors
- Stein, M., Hile, S. E., Weissensteiner, M. H., Lee, M., Zhang, S., Kejnovský, E., Kejnovská, I., Makova, K. D., & Eckert, K. A.
- Affiliations
- Pennsylvania State University (US)
- New York Medical College (US)
- Czech Academy of Sciences (CZ)
- Corresponding author
- Eckert, Kristin A.
- ORCID
- Venue
- DNA Repair
- Publisher
- Elsevier BV
- Published
- 2022-11
- Volume
- 119
- Pages
- 103402
- ISSN
- 1568-7856 (ISSN-L)
- 1568-7864
- PMC
- PMC9798401
- OpenAlex
- W4295073606
- Cited by
- 23
- References
- 62
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 2 · 2023: 8
- FWCI
- 1.39
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- DNA repair (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Touro Scholar (Touro College) (submittedVersion)
- Funders
- University of Pennsylvania
- Pennsylvania State University
- National Cancer Institute (R01CA237153)
- National Institute of General Medical Sciences (R01GM136684)
- National Institute of Environmental Health Sciences (R01ES014737, R56ES014737)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
- Keywords
- G-quadruplex, DNA polymerase fidelity, DNA polymerase delta, DNA polymerase eta, DNA polymerase kappa, non-B DNA structures, G-quadruplex topology, G-quadruplex stability, forward mutation assay, frameshift mutation, genome stability
- MeSH terms
- DNA, DNA-Directed DNA Polymerase, DNA Replication, Humans, Vascular Endothelial Growth Factor A, G-Quadruplexes
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