GO:0061849 telomeric G-quadruplex DNA binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0061849 (telomeric G-quadruplex DNA binding) is a molecular_function describing binding to stacked guanine-tetrad structures formed in telomeric DNA.
• Telomeric G-quadruplexes are non-canonical four-stranded DNA structures that regulate telomere maintenance and are recognized by dedicated proteins such as yeast Rap1 and human hnRNP A1/UP1.
• G-quadruplex-binding proteins and small-molecule ligands can be targeted with CRISPR-guided systems to study specific G-quadruplexes in living cells.
• The Ewing sarcoma protein (EWSR1) binds telomeric G-quadruplexes and regulates transcription of telomeric repeat-containing RNA (TERRA).
• Computational and biophysical methods (funnel-metadynamics, molecular rotors) reveal ligand binding modes and selectivity for human telomeric G-quadruplex DNA.
• Dysregulation of telomeric G-quadruplex recognition is linked to cancer and other diseases, making this term a focus for therapeutic development.
Description
GO:0061849, telomeric G-quadruplex DNA binding, is a Gene Ontology molecular_function term that describes the selective interaction of a protein or ligand with G-quadruplex DNA structures formed at telomeres. Telomeres are specialized nucleoprotein complexes at chromosome ends that protect genomic integrity, and their DNA contains tandem repeats rich in guanine, which can fold into four-stranded G-quadruplexes through Hoogsteen hydrogen bonding between guanine tetrads. Proteins that bind these structures are critical for telomere maintenance, replication, and transcriptional regulation of telomeric repeat-containing RNA (TERRA). Researchers study GO:0061849 because telomeric G-quadruplexes are emerging as therapeutic targets and as dynamic regulators of genome stability. The binding event is not merely structural; it can unfold or stabilize G-quadruplexes, recruit other factors, and influence telomerase access. Recent work has even used CRISPR-guided G-quadruplex-binding proteins and ligands to target specific G-quadruplexes in cells, demonstrating the functional importance of precise recognition. Understanding the molecular basis of telomeric G-quadruplex DNA binding therefore bridges structural biology, chemical biology, and gene regulation. This article synthesizes authoritative QuickGO annotation and verified PubMed literature to define the term, outline its mechanism, list key genes, and describe experimental models for functional studies.
telomeric G-quadruplex DNA binding At A Glance
| GO ID | GO:0061849 |
|---|---|
| GO term | telomeric G-quadruplex DNA binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to stacked guanine-tetrad structures in telomeric DNA |
| Definition source | QuickGO definition: Binding to telomeric G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad; stacking of guanine tetrads results in G-quadruplex DNA structures in telomeres. |
| Related structures | Guanine tetrad, G-quadruplex, telomere |
| Example binders | Yeast Rap1, human hnRNP A1/UP1, EWSR1, small-molecule ligands |
| Disease relevance | Cancer, telomere-related disorders |
What Is GO:0061849?
In our own words, GO:0061849 (telomeric G-quadruplex DNA binding) is the molecular function of selectively binding to G-quadruplex DNA structures located at telomeres. These structures arise when four guanine bases associate in a planar Hoogsteen-bonded arrangement called a guanine tetrad, and multiple tetrads stack to form a G-quadruplex. The binding event can be mediated by proteins or small molecules and may stabilize, unfold, or otherwise modulate the telomeric G-quadruplex.
Why Is telomeric G-quadruplex DNA binding Important in Cell Biology?
Telomeric G-quadruplex DNA binding is important because it directly influences telomere structure and function, which are central to chromosome stability and cellular lifespan. Proteins that recognize telomeric G-quadruplexes can regulate telomerase activity, TERRA transcription, and DNA replication through telomeric repeats. Moreover, small molecules and CRISPR-guided binders that target these structures are being developed as anticancer agents and as tools to dissect G-quadruplex biology.
• Regulates telomere maintenance and protects chromosome ends.
• Controls access of telomerase and other factors to telomeric DNA.
• Modulates transcription of TERRA, a non-coding RNA involved in telomere function.
• Provides a target for anticancer drug discovery via G-quadruplex ligands.
• Enables CRISPR-guided targeting of specific G-quadruplexes for functional studies.
• Involves proteins such as Rap1 and hnRNP A1/UP1 with roles in genome stability.
• Links structural biology of DNA to gene regulation and disease.
• Offers a paradigm for studying non-B DNA structures in vivo.
Molecular Mechanism of telomeric G-quadruplex DNA binding
Formation of telomeric G-quadruplex structures
In simple terms: Telomeric DNA can fold into a four-stranded knot called a G-quadruplex.
Telomeric DNA consists of tandem guanine-rich repeats that can fold into G-quadruplex structures, where four guanines form a planar guanine tetrad via Hoogsteen hydrogen bonds, and multiple tetrads stack to create a stable four-stranded structure. These structures are polymorphic and can adopt different topologies depending on conditions and sequence.
Recognition by telomeric proteins
In simple terms: Specific proteins recognize and bind the G-quadruplex shape.
Proteins such as the yeast telomeric protein Rap1 bind telomeric G-quadruplex DNA with structural specificity, as revealed by crystallographic and biochemical studies. In humans, hnRNP A1 and its UP1 domain bind and unfold human telomeric G-quadruplex DNA, facilitating processes like telomere replication.
Ligand binding and small-molecule recognition
In simple terms: Small molecules can also bind telomeric G-quadruplexes and are studied as drugs.
Small-molecule ligands, including red-emissive molecular rotors, preferentially recognize human telomeric G-quadruplex DNA, and their binding modes have been characterized by funnel-metadynamics simulations and spectroscopic methods. Such ligands are explored for cancer chemotherapy because they can stabilize G-quadruplexes and interfere with telomere maintenance.
CRISPR-guided targeting of specific G-quadruplexes
In simple terms: CRISPR can be used to deliver G-quadruplex-binding proteins to precise DNA locations.
A recent study demonstrated that CRISPR-guided G-quadruplex-binding proteins and ligands can target specific DNA G-quadruplexes in cells, enabling functional interrogation of individual G-quadruplex structures. This approach links the molecular function of telomeric G-quadruplex DNA binding to cellular outcomes.
Regulation of TERRA transcription by G-quadruplex binders
In simple terms: Some proteins that bind telomeric G-quadruplexes control TERRA RNA production.
The Ewing sarcoma protein (EWSR1) binds G-quadruplexes and regulates transcription of telomeric repeat-containing RNA (TERRA), thereby influencing telomere biology. This illustrates how telomeric G-quadruplex DNA binding can have downstream transcriptional consequences.
Key Genes Involved in GO:0061849 telomeric G-quadruplex DNA binding
The following genes and proteins have been experimentally linked to telomeric G-quadruplex DNA binding or its functional consequences.
| Gene | Major Role | Research Relevance |
|---|---|---|
| RAP1 (yeast) | Binds telomeric G-quadruplex DNA with structural specificity | Model for telomere protection and G-quadruplex recognition |
| HNRNPA1 | Binds and unfolds human telomeric G-quadruplex DNA via UP1 domain | Links G-quadruplex unfolding to telomere replication and stability |
| EWSR1 | Binds G-quadruplexes and regulates TERRA transcription | Connects G-quadruplex binding to non-coding RNA regulation |
| TERC | RNA component of telomerase; telomerase activity influenced by G-quadruplexes | Target for telomerase inhibition via G-quadruplex stabilization |
| TERT | Catalytic subunit of telomerase; access to telomeres modulated by G-quadruplexes | Cancer therapeutic target |
| TP53 | Tumor suppressor; G-quadruplexes in its promoter and telomeric regions | Indirect link to G-quadruplex biology in cancer |
| MYC | Oncogene with G-quadruplex-forming promoter; G-quadruplex ligands affect expression | Model for G-quadruplex-mediated transcriptional control |
| KRAS | Oncogene with G-quadruplex-forming regions | Potential target for G-quadruplex ligands |
| BCL2 | Anti-apoptotic gene with G-quadruplex in promoter | G-quadruplex ligand studies in cancer |
| C9orf72 | Hexanucleotide repeat expansions form G-quadruplexes | Neurodegeneration model for G-quadruplex binding |
| FUS | RNA/DNA-binding protein implicated in G-quadruplex interactions | Neurodegenerative disease relevance |
| TOP1 | Topoisomerase I interacts with G-quadruplex structures | DNA metabolism and G-quadruplex processing |
| BLM | RecQ helicase that resolves G-quadruplexes | Genome stability and telomere maintenance |
| WRN | RecQ helicase with G-quadruplex unwinding activity | Premature aging and telomere biology |
| POT1 | Shelterin component that binds telomeric ssDNA and may encounter G-quadruplexes | Telomere protection |
| TRF1 | Shelterin component binding telomeric dsDNA | Telomere length regulation |
| TRF2 | Shelterin component binding telomeric dsDNA | Telomere protection and G-quadruplex crosstalk |
| RAD51 | Recombinase that can interact with G-quadruplex DNA | Homologous recombination at telomeres |
How Is telomeric G-quadruplex DNA binding Regulated?
The binding of proteins and ligands to telomeric G-quadruplex DNA is regulated by multiple factors, including the local DNA sequence and topology, the presence of competing single-stranded DNA-binding proteins such as replication protein A, and post-translational modifications of G-quadruplex-binding proteins. Additionally, the transcription of TERRA, which can form G-quadruplexes and interact with telomeric proteins, is regulated by G-quadruplex-binding factors like EWSR1. Small molecules and CRISPR-guided systems can also modulate G-quadruplex recognition in a targeted manner.
telomeric G-quadruplex DNA binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| TERT | Cancer, telomerase activation | Knockout or point-mutation in cancer cell lines |
| HNRNPA1 | Telomere replication stress, cancer | Knockout and rescue with wild-type or unfolding-deficient mutants |
| EWSR1 | Ewing sarcoma, TERRA regulation | Knockout and overexpression in sarcoma cell lines |
| C9orf72 | ALS/FTD with G-quadruplex-forming repeats | Knock-in of repeat expansions in neurons |
| RAP1 (yeast) | Telomere protection model | Yeast knockout and point mutants |
Cancer
Telomeric G-quadruplex DNA binding is linked to cancer because G-quadruplex stabilization can inhibit telomerase and telomere maintenance in cancer cells. Small-molecule ligands that bind telomeric G-quadruplexes are being developed as anticancer agents, and their mechanisms have been studied using computational and biophysical approaches. Targeting specific G-quadruplexes with CRISPR-guided binders offers a precise way to probe their roles in cancer cell proliferation.
Neurodegeneration
G-quadruplex structures, including those formed by repeat expansions, are implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. Proteins that bind these structures may contribute to disease pathology, and understanding telomeric G-quadruplex DNA binding provides a framework for studying similar interactions in neurodegeneration.
Telomere-related disorders
Dysregulation of telomere maintenance, including altered G-quadruplex recognition, can lead to telomere dysfunction and premature aging syndromes. Proteins such as hnRNP A1/UP1 that unfold telomeric G-quadruplexes are important for telomere replication, and their dysfunction may contribute to telomere-related pathologies.
From telomeric G-quadruplex DNA binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does a candidate gene bind telomeric G-quadruplex DNA? | Knockout cell line with G-quadruplex pulldown or EMSA |
| Does a point mutation abolish G-quadruplex binding? | Point-mutation knock-in of the DNA-binding domain |
| Can a G-quadruplex-binding protein be targeted to a specific locus? | CRISPR-guided knock-in of a fusion protein |
| What is the effect of G-quadruplex ligand on telomere function? | Overexpression of telomerase and ligand treatment |
| How does G-quadruplex binding regulate TERRA? | Knockout of EWSR1 followed by RNA-seq |
| Does G-quadruplex stabilization affect cancer cell viability? | Overexpression of anti-apoptotic genes and ligand treatment |
How to Study the telomeric G-quadruplex DNA binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| EMSA | Protein-DNA binding affinity and specificity | Testing G-quadruplex binding by candidate proteins |
| Funnel-metadynamics | Ligand binding free energy and pathways | Computational ligand design for telomeric G-quadruplex |
| Fluorescence spectroscopy | Binding-induced fluorescence changes | Screening molecular rotors for G-quadruplex recognition |
| X-ray crystallography | Three-dimensional structure of protein-DNA complex | Structural basis of Rap1-G-quadruplex recognition |
| CRISPR-guided targeting | Locus-specific G-quadruplex function | In vivo targeting of specific G-quadruplexes |
| RNA-seq | Transcriptional changes including TERRA | EWSR1 knockout effects on TERRA |
| Proteomics | Protein interactors of telomeric G-quadruplexes | Identifying novel G-quadruplex-binding proteins |
| Cell viability assays | Cytotoxic effects of G-quadruplex ligands | Cancer drug discovery |
Biophysical binding assays
Electrophoretic mobility shift assays (EMSA), surface plasmon resonance, and isothermal titration calorimetry can measure binding affinity and specificity of proteins or ligands to telomeric G-quadruplex DNA. These methods are foundational for characterizing GO:0061849 activity.
Structural biology
X-ray crystallography and NMR spectroscopy provide atomic-level views of how proteins like yeast Rap1 recognize telomeric G-quadruplex DNA. Computational approaches such as funnel-metadynamics simulations complement experiments by revealing ligand binding pathways.
Fluorescence-based assays
Red-emissive molecular rotors and fluorescent probes can detect and quantify G-quadruplex binding in solution and in cells, enabling high-throughput screening of ligands.
CRISPR-guided targeting and functional genomics
CRISPR-guided G-quadruplex-binding proteins and ligands allow locus-specific interrogation of G-quadruplex function, and can be combined with RNA-seq or proteomics to assess downstream effects.
How CRISPR Can Be Used to Study GO:0061849 telomeric G-quadruplex DNA binding
Knockout
CRISPR knockout of genes encoding telomeric G-quadruplex-binding proteins (e.g., HNRNPA1, EWSR1) can reveal their roles in telomere maintenance and TERRA regulation. Knockout cell lines are essential for loss-of-function studies of GO:0061849.
Point Mutation
Point mutations in the DNA-binding domain of proteins like Rap1 or hnRNP A1 can abolish G-quadruplex binding without affecting protein stability, allowing precise structure-function analysis. CRISPR-mediated point-mutation knock-in is ideal for such studies.
Knock-in
Knock-in of tagged or fluorescently labeled G-quadruplex-binding proteins enables live-cell imaging and locus-specific targeting when combined with CRISPR-guided systems. This approach helps visualize telomeric G-quadruplex dynamics.
Overexpression
Overexpression of G-quadruplex-binding proteins or ligands can amplify their effects on telomere function and TERRA transcription, providing gain-of-function models for drug testing. CRISPR activation (CRISPRa) can achieve controlled overexpression.
How EDITGENE Supports telomeric G-quadruplex DNA binding Research
Researchers studying telomeric G-quadruplex DNA binding-related genes often need to determine whether a candidate gene is causally involved in G-quadruplex recognition, telomere maintenance, or disease. EDITGENE provides comprehensive CRISPR-based services to generate precisely engineered cell models for such functional studies.
Contact EDITGENE today to design your custom CRISPR model for telomeric G-quadruplex DNA binding research.
Frequently Asked Questions About telomeric G-quadruplex DNA binding
What is telomeric G-quadruplex DNA binding?
It is the molecular function (GO:0061849) of binding to G-quadruplex structures formed by stacked guanine tetrads in telomeric DNA.
What genes are involved in telomeric G-quadruplex DNA binding?
Key genes include RAP1, HNRNPA1, EWSR1, and shelterin components such as POT1, TRF1, and TRF2.
How is telomeric G-quadruplex DNA binding studied?
Common methods include EMSA, X-ray crystallography, funnel-metadynamics simulations, fluorescence spectroscopy, and CRISPR-guided targeting.
Why is telomeric G-quadruplex DNA binding important in cancer?
G-quadruplex stabilization can inhibit telomerase and telomere maintenance, making it a target for anticancer drug development.
What proteins bind telomeric G-quadruplex DNA?
Examples include yeast Rap1, human hnRNP A1/UP1, and the Ewing sarcoma protein EWSR1.
Can CRISPR be used to target telomeric G-quadruplexes?
Yes, CRISPR-guided G-quadruplex-binding proteins and ligands have been used to target specific G-quadruplexes in cells.
What is the role of TERRA in telomeric G-quadruplex DNA binding?
TERRA transcription is regulated by G-quadruplex-binding proteins such as EWSR1, linking G-quadruplex recognition to telomere function.
How do small molecules bind telomeric G-quadruplex DNA?
Ligands can stack on guanine tetrads, and their binding modes are revealed by simulations and spectroscopy.
What diseases are associated with telomeric G-quadruplex DNA binding?
Cancer, neurodegeneration, and telomere-related disorders are linked to G-quadruplex biology.
What experimental models are used to study telomeric G-quadruplex DNA binding?
Knockout, point-mutation, knock-in, and overexpression cell models, as well as yeast and human cell lines, are commonly used.
Conclusion
GO:0061849 (telomeric G-quadruplex DNA binding) is a molecular function that governs the recognition of four-stranded guanine-rich structures at chromosome ends. It is mediated by proteins such as Rap1, hnRNP A1/UP1, and EWSR1, and can be targeted by small molecules and CRISPR-guided systems. Understanding this function is critical for telomere biology and for developing therapies against cancer and other diseases. EDITGENE provides the CRISPR cell models and bioinformatics support needed to dissect the causal roles of G-quadruplex-binding genes in health and disease.
References
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