GO:0043047 single-stranded telomeric DNA binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0043047 (single-stranded telomeric DNA binding) is a molecular function defined as binding to single-stranded telomere-associated DNA.
• Key proteins include Cdc13 in Saccharomyces cerevisiae, and the CST complex (CTC1, STN1, TEN1) and RPA in humans.
• These proteins protect telomeric ssDNA, regulate telomerase access, and facilitate lagging-strand replication.
• Dysfunction of ssDNA-binding proteins is linked to telomere diseases such as dyskeratosis congenita and cancer.
• G-quadruplex structures in telomeric ssDNA can affect protein binding and are studied using biophysical methods.
• CRISPR-based models (knockout, point mutation, knock-in, overexpression) enable functional dissection of these proteins.
Description
Single-stranded telomeric DNA binding (GO:0043047) is a molecular function that enables proteins to recognize and bind the single-stranded G-rich overhang at chromosome ends. This activity is essential for telomere protection, replication, and length regulation. The telomeric overhang is a substrate for telomerase and a target for DNA damage response, making its binding proteins critical guardians of genome stability. Researchers study this function to understand aging, cancer, and telomere-related diseases. The term is distinct from double-stranded telomeric DNA binding and is mediated by specialized ssDNA-binding proteins such as Cdc13 in yeast and the CST complex in humans.
single-stranded telomeric DNA binding At A Glance
| GO ID | GO:0043047 |
|---|---|
| GO term | single-stranded telomeric DNA binding |
| Ontology | molecular_function |
| Synonym | telomeric ssDNA binding |
| Major function | Binding to single-stranded telomere-associated DNA |
| Definition source | QuickGO |
| Related proteins | Cdc13, CST complex (CTC1, STN1, TEN1), RPA |
| Associated processes | Telomere maintenance, telomerase regulation, lagging-strand replication |
What Is GO:0043047?
GO:0043047 (single-stranded telomeric DNA binding) is defined as the binding to single-stranded telomere-associated DNA. This function is exhibited by proteins that interact with the G-rich single-stranded overhang at the ends of linear chromosomes. It is a molecular function term in the Gene Ontology, with the synonym telomeric ssDNA binding.
Why Is single-stranded telomeric DNA binding Important in Cell Biology?
Single-stranded telomeric DNA binding is crucial for maintaining genome integrity because it protects chromosome ends from being recognized as DNA damage and regulates telomerase-mediated elongation. Proteins with this function, such as Cdc13 and CST, coordinate telomere replication and prevent inappropriate recombination. Defects in these proteins lead to telomere shortening, genomic instability, and diseases like dyskeratosis congenita and cancer. Understanding this function provides insights into aging and potential therapeutic targets.
• Protects telomeric ssDNA from degradation and DNA damage response.
• Regulates telomerase access to the 3' overhang.
• Facilitates lagging-strand DNA replication at telomeres.
• Prevents inappropriate recombination and fusion of chromosome ends.
• Mutations in CST components cause telomere biology disorders.
• G-quadruplex structures in telomeric ssDNA modulate protein binding.
• Involved in cellular aging and senescence.
• Potential target for anti-cancer therapies.
• Studied in plants for telomere maintenance.
• Biophysical studies reveal conformational dynamics of telomeric ssDNA.
Molecular Mechanism of single-stranded telomeric DNA binding
Recognition of the G-rich overhang
In simple terms: Proteins recognize the single-stranded tail at chromosome ends.
Proteins such as Cdc13 in Saccharomyces cerevisiae specifically bind the G-rich single-stranded telomeric DNA overhang. This binding is sequence-specific and involves electrostatic interactions with the phosphate backbone and base-specific contacts. The overhang is generated by resection of the C-rich strand and serves as a substrate for telomerase.
CST complex assembly
In simple terms: A three-protein complex forms on the telomeric ssDNA to protect it.
In humans, the CST complex (CTC1, STN1, TEN1) binds single-stranded telomeric DNA with high affinity. CST acts as a specialized processivity factor for DNA polymerase alpha during lagging-strand synthesis. It also regulates telomerase by limiting its access to the 3' end.
RPA-like complexes in telomere maintenance
In simple terms: RPA and similar proteins help manage the single-stranded DNA at telomeres.
Replication protein A (RPA) binds single-stranded DNA during replication and is involved in telomere maintenance. RPA-like complexes including CST serve as processivity factors for polymerases. In plants, single-stranded DNA-binding proteins play analogous roles at telomeres.
G-quadruplex formation and dynamics
In simple terms: The single-stranded DNA can fold into four-stranded structures that affect binding.
Human telomeric single-stranded DNA can form G-quadruplex structures, which are stabilized by potassium ions. These structures undergo slow conformational rearrangements that affect accessibility to binding proteins. G-quadruplexes may regulate telomerase activity and protein binding.
Regulation by phosphorylation and protein interactions
In simple terms: Chemical modifications and partner proteins control when and how binding occurs.
Cdc13 is regulated by phosphorylation and interacts with Stn1 and Ten1 to form a complex. In humans, CST complex formation is essential for its function and is regulated by cell cycle-dependent expression. These regulatory mechanisms ensure proper telomere maintenance.
Key Genes Involved in GO:0043047 single-stranded telomeric DNA binding
The following genes encode proteins that exhibit single-stranded telomeric DNA binding activity or are directly involved in this function.
| Gene | Major Role | Research Relevance |
|---|---|---|
| CDC13 | Binds single-stranded telomeric DNA in S. cerevisiae | Model for sequence-specific ssDNA binding |
| CTC1 | Component of human CST complex | Mutations cause dyskeratosis congenita |
| STN1 | Component of CST complex | Regulates telomerase and replication |
| TEN1 | Component of CST complex | Protects telomeric ssDNA |
| RPA1 | Binds ssDNA during replication | Involved in telomere replication |
| RPA2 | Subunit of RPA complex | Facilitates lagging-strand synthesis |
| RPA3 | Subunit of RPA complex | Essential for ssDNA binding |
| POT1 | Binds telomeric ssDNA in shelterin | Protects telomeres from damage response |
| TPP1 | Partners with POT1 | Regulates telomerase recruitment |
| TERF1 | Binds double-stranded telomeric DNA | Interacts with ssDNA-binding proteins |
| TERF2 | Binds double-stranded telomeric DNA | Shelterin component |
| TERT | Telomerase reverse transcriptase | Elongates telomeres using ssDNA substrate |
| TERC | Telomerase RNA component | Template for telomere synthesis |
| STN1 (plant) | Plant CST component | Telomere maintenance in plants |
| CTC1 (plant) | Plant CST component | Telomere protection in plants |
| TEN1 (plant) | Plant CST component | Telomere replication |
| DNA2 | Nuclease involved in telomere processing | Generates ssDNA overhang |
How Is single-stranded telomeric DNA binding Regulated?
The activity of single-stranded telomeric DNA-binding proteins is regulated at multiple levels. In Saccharomyces cerevisiae, Cdc13 is phosphorylated in a cell cycle-dependent manner, affecting its binding and interactions. The human CST complex is regulated by its subunit expression and assembly, and its binding to telomeric ssDNA is influenced by G-quadruplex structures. Additionally, post-translational modifications such as phosphorylation and ubiquitination modulate the function of RPA and CST during replication stress.
single-stranded telomeric DNA binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| CTC1 | Dyskeratosis congenita | Knockout in human cell lines |
| STN1 | Dyskeratosis congenita | Point mutation knock-in |
| TEN1 | Dyskeratosis congenita | Overexpression and knockout |
| POT1 | Cancer, melanoma | Conditional knockout in mouse |
| RPA1 | Cancer, replication stress | Knockdown and overexpression |
Dyskeratosis congenita and telomere biology disorders
Mutations in CST complex genes (CTC1, STN1, TEN1) cause dyskeratosis congenita, a bone marrow failure syndrome characterized by short telomeres. These mutations impair single-stranded telomeric DNA binding, leading to telomere uncapping and DNA damage.
Cancer
Altered expression of ssDNA-binding proteins is observed in various cancers. Overexpression of CST components can promote telomere maintenance and cancer cell survival. Conversely, loss of POT1, a telomeric ssDNA-binding protein, leads to telomere dysfunction and genomic instability, which can drive tumorigenesis.
Aging and degenerative diseases
Telomere shortening and dysfunction are hallmarks of aging. Defects in single-stranded telomeric DNA binding accelerate telomere erosion and cellular senescence. This contributes to age-related pathologies such as pulmonary fibrosis and aplastic anemia.
From single-stranded telomeric DNA binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of CTC1 affect telomere length? | CRISPR knockout of CTC1 in HeLa cells |
| How do point mutations in STN1 affect ssDNA binding? | Knock-in of patient mutations |
| Can overexpression of TEN1 rescue telomere defects? | Overexpression in patient fibroblasts |
| What is the role of Cdc13 phosphorylation? | Point mutation in S. cerevisiae CDC13 |
| How does POT1 binding affect telomere protection? | Inducible knockout in mouse embryonic fibroblasts |
| Does RPA depletion cause replication stress at telomeres? | siRNA knockdown in human cells |
How to Study the single-stranded telomeric DNA binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| EMSA | Protein-ssDNA binding affinity | In vitro binding studies |
| Single-molecule FRET | Conformational dynamics | G-quadruplex studies |
| ChIP | In vivo protein occupancy | Telomere binding mapping |
| CRISPR knockout | Gene function loss | Telomere phenotype analysis |
| CRISPR knock-in | Mutant protein expression | Disease mutation modeling |
| Overexpression | Gain-of-function effects | Rescue experiments |
| Telomere length assay (TRF) | Telomere length | Assessing dysfunction |
| Immunofluorescence | Protein localization | Telomere co-localization |
Electrophoretic mobility shift assay (EMSA)
EMSA is used to measure direct binding of proteins to single-stranded telomeric DNA. For example, recombinant Cdc13p was shown to bind specifically to telomeric ssDNA in vitro. This method allows determination of binding affinity and specificity.
Single-molecule FRET and biophysical assays
Single-molecule FRET and other biophysical techniques reveal conformational dynamics of telomeric ssDNA and its interactions with proteins. These methods have been used to study G-quadruplex rearrangement induced by potassium.
Chromatin immunoprecipitation (ChIP)
ChIP can detect proteins bound to telomeric DNA in vivo. It has been used to map CST complex binding at telomeres. Coupled with quantitative PCR, it provides information on occupancy and regulation.
CRISPR-based functional genomics
CRISPR knockout, knock-in, and overexpression models enable functional dissection of genes encoding ssDNA-binding proteins. These approaches can reveal causal roles in telomere maintenance and disease.
How CRISPR Can Be Used to Study GO:0043047 single-stranded telomeric DNA binding
Knockout
CRISPR knockout of genes encoding single-stranded telomeric DNA-binding proteins (e.g., CTC1, STN1, TEN1) can reveal their essential roles in telomere maintenance. Knockout cell lines often exhibit telomere shortening, increased DNA damage, and growth defects.
Point Mutation
Introducing disease-associated point mutations (e.g., in CTC1 or STN1) via CRISPR knock-in allows modeling of dyskeratosis congenita and studying the impact on ssDNA binding. These models help dissect structure-function relationships.
Knock-in
Knock-in of tagged versions (e.g., GFP or HA) of ssDNA-binding proteins enables live-cell imaging and proteomic analysis. This approach can track protein dynamics at telomeres.
Overexpression
CRISPR activation (CRISPRa) or cDNA overexpression can elevate levels of ssDNA-binding proteins to study gain-of-function effects, such as telomere elongation or protection against damage.
How EDITGENE Supports single-stranded telomeric DNA binding Research
Researchers studying single-stranded telomeric DNA binding-related genes often need to determine whether a candidate gene is causally involved in telomere maintenance or disease. EDITGENE provides comprehensive CRISPR services to generate precisely engineered cell models for such functional studies.
Contact EDITGENE today to design your custom CRISPR model for single-stranded telomeric DNA binding research.
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| POT1 Knockout HEK293 Cell Line | EDJ-KQ7612 | Human | 25913 | Details Get a Quote |
| STN1 Knockout HEK293 Cell Line | EDJ-KQ15545 | Human | 79991 | Details Get a Quote |
| POT1 Knockout HCT 116 Cell Line | EDJ-KQ34268 | Human | 25913 | Details Get a Quote |
| POT1 Knockout HeLa Cell Line | EDJ-KQ34269 | Human | 25913 | Details Get a Quote |
| STN1 Knockout A-549 Cell Line | EDJ-KQ46394 | Human | 79991 | Details Get a Quote |
| STN1 Knockout HCT 116 Cell Line | EDJ-KQ46395 | Human | 79991 | Details Get a Quote |
| STN1 Knockout HeLa Cell Line | EDJ-KQ46396 | Human | 79991 | Details Get a Quote |
| RAD50 Knockout HEK293 Cell Line | EDJ-KQ50932 | Human | 10111 | Details Get a Quote |
| RAD50 Knockout HeLa Cell Line | EDJ-KQ55321 | Human | 10111 | Details Get a Quote |
| RAD50 Knockout A-549 Cell Line | EDJ-KQ63804 | Human | 10111 | Details Get a Quote |
| POT1 Knockout A-549 Cell Line | EDJ-KQ64337 | Human | 25913 | Details Get a Quote |
| RAD50 Knockout HCT 116 Cell Line | EDJ-KQ72262 | Human | 10111 | Details Get a Quote |
Frequently Asked Questions About single-stranded telomeric DNA binding
What is single-stranded telomeric DNA binding?
It is a molecular function (GO:0043047) where proteins bind to the single-stranded G-rich overhang at chromosome ends.
What genes are involved in single-stranded telomeric DNA binding?
Key genes include CDC13 in yeast, and CTC1, STN1, TEN1, POT1, and RPA in humans.
What is the role of CST complex in telomeres?
CST (CTC1-STN1-TEN1) binds telomeric ssDNA, protects it, and regulates telomerase and replication.
How is single-stranded telomeric DNA binding studied?
Common methods include EMSA, ChIP, single-molecule FRET, and CRISPR-based functional assays.
What diseases are associated with defects in this function?
Dyskeratosis congenita, cancer, and age-related disorders are linked to mutations in CST and POT1.
What is the difference between POT1 and CST?
POT1 is part of shelterin and binds telomeric ssDNA to protect it, while CST is a specialized complex for replication and telomerase regulation.
Can CRISPR be used to study single-stranded telomeric DNA binding?
Yes, CRISPR knockout, knock-in, and overexpression models enable functional studies of these proteins.
What is the structure of telomeric ssDNA?
It is a G-rich single strand that can form G-quadruplex structures, which are dynamic and regulated by ions.
How does Cdc13 bind telomeric DNA?
Cdc13 specifically recognizes the G-rich telomeric ssDNA via its OB-fold domains.
Why is single-stranded telomeric DNA binding important for aging?
It protects telomeres from degradation; its dysfunction leads to telomere shortening, a hallmark of aging.
Conclusion
Single-stranded telomeric DNA binding (GO:0043047) is a fundamental molecular function that safeguards chromosome ends and regulates telomere maintenance. Proteins such as Cdc13, CST, and POT1 are central to this activity, and their dysfunction is linked to human diseases including dyskeratosis congenita and cancer. Continued research using advanced CRISPR models and biophysical methods will further illuminate the mechanisms and therapeutic potential of targeting these interactions.
References
- 1. Luo M et al.. 2020. Single-stranded DNA-binding proteins in plant telomeres.. Int J Biol Macromol 165(Pt A):1463-1467 PMID: 32998016
- 2. Smith EM et al.. 2020. Structural biology of telomeres and telomerase.. Cell Mol Life Sci 77(1):61-79 PMID: 31728577
- 3. Lescalet G et al.. 2026. Single-stranded DNA-binding proteins at healthy and diseased telomeres.. Trends Biochem Sci 51(2):125-141 PMID: 41506931
- 4. Barbour AT et al.. 2023. RPA-like single-stranded DNA-binding protein complexes including CST serve as specialized processivity factors for polymerases.. Curr Opin Struct Biol 81:102611 PMID: 37245465
- 5. Rhodes D et al.. 2002. Telomere architecture.. EMBO Rep 3(12):1139-45 PMID: 12475927
- 6. Lin YC et al.. 2001. Specific binding of single-stranded telomeric DNA by Cdc13p of Saccharomyces cerevisiae.. J Biol Chem 276(27):24588-93 PMID: 11309395
- 7. Olson CL et al.. 2024. Guardians of the Genome: How the Single-Stranded DNA-Binding Proteins RPA and CST Facilitate Telomere Replication.. Biomolecules 14(3) PMID: 38540683
- 8. Lacen AN et al.. 2024. Slow G-Quadruplex Conformation Rearrangement and Accessibility Change Induced by Potassium in Human Telomeric Single-Stranded DNA.. J Phys Chem B 128(25):5950-5965 PMID: 38875355
