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The non-B DNA secondary structure known as G-quadruplex (G4) DNA can form in gene-regulatory regions of the human genome. Organic small molecules, so called G4-ligands, which bind and stabilize G4 DNA structures, have emerged as potential therapeutic agents and as chemical probes to study the cellular functions of these secondary DNA conformations. A major challenge, however, is their lack of selectively recognising different G4 structures, which hampers both their further development as therapeutics and their utility as research tools. This limitation can be addressed by linking the G4-ligand to a guide oligonucleotide, complementary to the flanking sequence of the target G4, a strategy called G4-ligand-conjugated oligonucleotides (GL-Os). Here, the G4-ligand used in the GL-O strategy is investigated by altering its physiochemical properties, including size and charge, and evaluating its potency using biochemical and biological assays. The results reveal a strong influence of the G4-ligand on the conjugates' ability to bind and stabilize the target G4 DNA. In particular, a larger and charged G4-ligand enhances both binding and stabilization of the target. However, increasing the G4-ligand potency may also increase off-target G4 binding, highlighting the need for a balanced G4-ligand potency to ensure high GL-O specificity for individual G4 structures.

G-quadruplex (G4) structures are non-canonical DNA and RNA conformations formed in guanine-rich regions that play roles in gene regulation, genome stability, and RNA processing. However, targeting the approximately 700,000 G4s in the human genome with high specificity remains challenging due to their structural similarities. Despite their biological significance, this inability to selectively study or manipulate individual G4s presents a significant barrier to understanding their distinct roles in human cells and complicates efforts to dissect their contributions to cellular processes.

To address this limitation, we developed a strategy based on click chemistry to covalently link short single-stranded oligonucleotides (Os) to G4 ligands (GLs). This approach combines the stabilising properties of G4 ligands with the sequence specificity of guide oligonucleotides to create G4-ligand-oligonucleotide (GL-O) conjugates. The oligonucleotide forms double-stranded DNA (dsDNA) with the flanking region of the target G4, ensuring selective binding and stabilisation of the desired G4 structure. Through biophysical and biochemical assays, we demonstrated that this approach enables the selective stabilisation of individual target G4s, highlighting its utility for studying specific G4 structures.

In refining the GL-O platform, we systematically evaluated various linker configurations. This work demonstrated that longer and more flexible linkers enhance the adaptability of GL-O conjugates, allowing efficient targeting of G4s with varying distances between the G4-forming region and the complementary oligonucleotide binding sequence. This insight is particularly valuable for addressing steric hindrances and expanding the range of targetable G4 structures.

Additionally, we explored the broader principles of G4 ligand design by focusing on dispersion forces and electrostatic interactions. Synthesising heterocyclic G4 ligands and studying their interactions with G4s showed that dispersion components in arene-arene interactions and electron-deficient electrostatics are central to achieving high-affinity binding and stabilisation. These findings enhance the GL-O approach by providing a framework to fine-tune the stabilisation effect of the GL-Os, potentially reducing off-target effects.

In parallel, we pursued a separate project that examined G4 structures within human mitochondrial DNA (mtDNA), aiming to elucidate their roles in cellular function. Human mtDNA contains regions that have been predicted to form G4 structures in silico. We mapped these mtDNA G4s using high-resolution techniques and demonstrated their formation in vivo. Stabilisation or replication stalling increases their formation, potentially contributing to mitochondrial dysfunction and genomic instability in disease. 

Together, these findings advance our understanding of G4 biology, from selective targeting strategies to the unique dynamics of mitochondrial G4s, offering valuable insights into the biological roles of G4s in maintaining genome stability and regulating cellular processes.

G-quadruplex (G4) DNA structures are noncanonical secondary structures found in key regulatory regions of the genome, including oncogenic promoters and telomeres. Small molecules, known as G4 ligands, capable of stabilizing G4s hold promise as chemical probes and therapeutic agents. Nevertheless, achieving precise specificity for individual G4 structures within the human genome remains a significant challenge. To address this, we expand upon G4-ligand-conjugated oligonucleotides (GL-Os), a modular platform combining the stabilizing properties of G4-ligands with the sequence specificity of guide DNA oligonucleotides. Central to this strategy is the linker that bridges the G4 ligand and the guide oligonucleotide. In this study, we develop multiple conjugation strategies for the GL-Os that enabled a systematic investigation of the linker in both chemical composition and length, enabling a thorough assessment of their impact on targeting oncogenic G4 DNA. Biophysical, biochemical, and computational evaluations revealed GL-Os with optimized linkers that exhibited enhanced binding to target G4s, even under thermal or structural stress. Notably, longer linkers broadened the range of targetable sequences without introducing steric hindrance, thereby enhancing the platform’s applicability across diverse genomic contexts. These findings establish GL-Os as a robust and versatile tool for the selective targeting of individual G4s. By facilitating precise investigations of G4 biology, this work provides a foundation for advancing G4-targeted therapeutic strategies and exploring their role in disease contexts.

Mitochondrial DNA (mtDNA) stability, essential for cellular energy production, relies on DNA polymerase gamma (POLγ). Here, we show that the POLγ Y951N disease-causing mutation induces replication stalling and severe mtDNA depletion. However, unlike other POLγ disease-causing mutations, Y951N does not directly impair exonuclease activity and only mildly affects polymerase activity. Instead, we found that Y951N compromises the enzyme’s ability to efficiently toggle between DNA synthesis and degradation, and is thus a patient-derived mutation with impaired polymerase-exonuclease switching. These findings provide insights into the intramolecular switch when POLγ proofreads the newly synthesized DNA strand and reveal a new mechanism for causing mitochondrial DNA instability.

G-Quadruplex (G4) DNA structures are important regulatory elements in central biological processes. Small molecules that selectively bind and stabilize G4 structures have therapeutic potential, and there are currently >1000 known G4 ligands. Despite this, only two G4 ligands ever made it to clinical trials. In this work, we synthesized several heterocyclic G4 ligands and studied their interactions with G4s (e.g., G4s from the c-MYC, c-KIT, and BCL-2 promoters) using biochemical assays. We further studied the effect of selected compounds on cell viability, the effect on the number of G4s in cells, and their pharmacokinetic properties. This identified potent G4 ligands with suitable properties and further revealed that the dispersion component in arene-arene interactions in combination with electron-deficient electrostatics is central for the ligand to bind with the G4 efficiently. The presented design strategy can be applied in the further development of G4-ligands with suitable properties to explore G4s as therapeutic targets.

G-quadruplex (G4) DNA structures are prevalent secondary DNA structures implicated in fundamental cellular functions, such as replication and transcription. Furthermore, G4 structures are directly correlated to human diseases such as cancer and have been highlighted as promising therapeutic targets for their ability to regulate disease-causing genes, e.g., oncogenes. Small molecules that bind and stabilize these structures are thus valuable from a therapeutic perspective and helpful in studying the biological functions of the G4 structures. However, there are hundreds of thousands of G4 DNA motifs in the human genome, and a long-standing problem in the field is how to achieve specificity among these different G4 structures. Here, we developed a strategy to selectively target an individual G4 DNA structure. The strategy is based on a ligand that binds and stabilizes G4s without selectivity, conjugated to a guide oligonucleotide, that specifically directs the G4-Ligand-conjugated oligo (GL-O) to the single target G4 structure. By employing various biophysical and biochemical techniques, we show that the developed method enables the targeting of a unique, specific G4 structure without impacting other off-target G4 formations. Considering the vast amount of G4s in the human genome, this represents a promising strategy to study the presence and functions of individual G4s but may also hold potential as a future therapeutic modality.

Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.

Replication forks often stall at damaged DNA. To overcome these obstructions and complete the DNA duplication in a timely fashion, replication can be restarted downstream of the DNA lesion. In mammalian cells, this repriming of replication can be achieved through the activities of primase and polymerase PrimPol. PrimPol is stimulated in DNA synthesis through interaction with PolDIP2, however the exact mechanism of this PolDIP2-dependent stimulation is still unclear. Here, we show that PrimPol uses a flexible loop to interact with the C-terminal ApaG-like domain of PolDIP2, and that this contact is essential for PrimPol's enhanced processivity. PolDIP2 increases primer-template and dNTP binding affinities of PrimPol, which concomitantly enhances its nucleotide incorporation efficiency. This stimulation is dependent on a unique arginine cluster in PolDIP2. Since the polymerase activity of PrimPol alone is very limited, this mechanism, where the affinity for dNTPs gets increased by PolDIP2 binding, might be critical for the in vivo function of PrimPol in tolerating DNA lesions at physiological nucleotide concentrations.