Variation in G-Quadruplex Sequence and Topology Differentially Impacts Human DNA Polymerase Fidelity

Authors

MaryElizabeth Stein, Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA, USA.
Suzanne E. Hile, Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA, USA.
Matthias H. Weissensteiner, Department of Biology, Penn State University Eberly College of Science, University Park, PA, USA.
Marietta Lee, Department of Biochemistry & Molecular Biology, New York Medical College, Valhalla, NY, USA.Follow
Sufang Zhang, Department of Biochemistry & Molecular Biology, New York Medical College, Valhalla, NY, USA.
Eduard Kejnovský, Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
Iva Kejnovská, Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
Kateryna D. Makova, Department of Biology, Penn State University Eberly College of Science, University Park, PA, USA.
Kristin A. Eckert, Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA, USA. Electronic address: kae4@psu.edu.

Author Type(s)

Faculty

DOI

10.1016/j.dnarep.2022.103402

Journal Title

DNA Repair

First Page

103402

Document Type

Article

Publication Date

11-1-2022

Department

Biochemistry and Molecular Biology

Abstract

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.

Recommended Citation

Stein, M., Hile, S. E., Weissensteiner, M. H., Lee, M., Zhang, S., Kejnovský, E., Kejnovská, I., Makova, K. D., & Eckert, K. A. (2022). Variation in G-Quadruplex Sequence and Topology Differentially Impacts Human DNA Polymerase Fidelity. DNA Repair, 119, 103402. https://doi.org/10.1016/j.dnarep.2022.103402