Author

Jean-Louis Mergny

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Open access Aug 2026

Introduction of a Double-Headed Nucleotide Into G-Quadruplex DNA: Position-Dependent Stabilization and Structural Insights.

G-quadruplexes are structurally diverse nucleic acid motifs with important biological properties as well as emerging applications in biotechnology and therapeutics. Here, we investigate whether a double-headed bis-guanine (G) nucleotide, GG-a substantial deviation from canonical nucleic acid architecture-can be accommodated within G-quadruplex structures and how its effects depend on sequence context and topology. Using a combination of circular dichroism (CD) spectroscopy, thermal denaturation analysis, UV thermal differential spectroscopy (TDS), fluorescence light-up assays, polyacrylamide gel electrophoresis (PAGE) analysis, and molecular dynamics (MD) simulations, we show that GG can substitute two consecutive guanosines in G-quadruplex-forming oligonucleotides (ONs) and directly participate in G-tetrad formation, but with strong sequence- and position-dependent consequences. GG incorporation is best tolerated in parallel G-quadruplexes and at G-tetrad steps with low native torsional twist, where local unwinding can be accommodated. In a tetramolecular TG4T system, GG positioned near the 3'-end of the G-stack preserved parallel G-quadruplex topology while providing significant thermal stabilization (+21°C). In the antiparallel thrombin-binding aptamer (TBA), a single GG incorporation yielded exceptional stabilization (+34°C) but was accompanied by altered topological signatures. Together, the results presented herein establish GG as a powerful but context-dependent G-quadruplex stabilizer and define design principles for its use in engineered G-quadruplexes and aptamer development.

Krista Urup, Peter Reinholdt, Kasper M. Beck et al. · Chemistry · 0 citations

Open access Jul 2026

G‑quadruplexes as regulatory platforms for human transcription factors: insights from ChIP-seq data

G-quadruplexes (G4s) are non-canonical DNA structures with important regulatory functions. While several transcription factors have been shown to interact with G4s, a comprehensive understanding of this interaction network remains elusive. Here, we integrated genome-wide predictions of highly stable G-quadruplex sequences with 32,817 ChIP-seq datasets from ChIP-Atlas to systematically map transcription factors and transcription-associated chromatin proteins linked to G4-rich regions in the human genome. Highly stable G4 motifs are non-randomly distributed, showing strong enrichment in gene-dense chromosomes, at promoters, regulatory regions, and repeat elements. Integration with transcription factor binding profiles revealed a broad spectrum of G4-associated proteins, including established interactors such as STAT3, TP53 and CTCF, and the transcription-associated chromatin regulator BRD4, as well as previously unrecognized candidates such as REST, NR3C1, FLI1, and HSF1. Unexpectedly, only a minority of transcription factors were consistently depleted from G4 regions. Our results indicate that G-quadruplex-prone sequences represent a common genomic feature associated with a number of human transcription factors and chromatin-associated regulatory proteins and support a model in which G4-rich regions act as selective regulatory scaffolds shaping transcription factor occupancy and gene regulation.

Karolína Drápalová, Michaela Dobrovolná, Filip Kledus et al. · BMC Genomics · 0 citations