GO:0032138 single base insertion or deletion binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0032138 defines the molecular function of binding to double-stranded DNA containing a single base insertion or deletion.
• The yeast MutS homolog heterodimer MSH2-MSH3 was the first complex shown to bind insertion/deletion mismatches, providing the founding biochemical evidence for this GO term.
• Single base insertion or deletion binding is a critical early step in DNA mismatch repair, which maintains genome stability and prevents microsatellite instability.
• Defects in genes encoding insertion/deletion binding proteins are linked to cancer predisposition, neurodevelopmental disorders, and congenital disease.
• Structural variation such as NRXN1 deletions and Y-chromosome gene disruptions can be modeled using CRISPR to study the functional consequences of altered DNA binding.
• Research methods for this function include electrophoretic mobility shift assays, surface plasmon resonance, and CRISPR-based knockout or knock-in models.
Description
GO:0032138, single base insertion or deletion binding, is a molecular function term that describes the binding of a protein or protein complex to a double-stranded DNA region containing a single base insertion or deletion. This activity is essential for recognizing DNA mismatches that arise during replication, recombination, or damage repair, and it represents the first step in mismatch repair pathways that preserve genomic integrity. The founding biochemical evidence for this function came from the yeast heterodimer MSH2-MSH3, which was shown to bind insertion/deletion mismatches in vitro. Since then, related proteins in higher eukaryotes have been implicated in a wide range of biological processes, from spermatogenesis to neurodevelopment. Understanding this GO term is therefore central to interpreting how cells detect and respond to small insertions and deletions, which are among the most common forms of genetic variation in human disease.
single base insertion or deletion binding At A Glance
| GO ID | GO:0032138 |
|---|---|
| GO term | single base insertion or deletion binding |
| Ontology | molecular_function |
| Synonym | single base insertion binding |
| Definition | Binding to a double-stranded DNA region containing a single base insertion or deletion. |
| Major function | Recognition of insertion/deletion mismatches in DNA, initiating mismatch repair and maintaining genome stability. |
| Founding evidence | Yeast MSH2-MSH3 heterodimer binds insertion/deletion mismatches. |
| Related diseases | Cancer, neurodevelopmental disorders, congenital glaucoma, spinal muscular atrophy. |
| Research methods | EMSA, SPR, CRISPR knockout/knock-in, bioinformatics analysis. |
What Is GO:0032138?
In simple terms, GO:0032138 describes the ability of a protein to physically attach to a double-stranded DNA molecule that contains a single extra base (insertion) or a single missing base (deletion) on one strand. This binding event is non-covalent and sequence-independent in the sense that it recognizes the structural distortion caused by the insertion or deletion rather than a specific DNA sequence. The QuickGO definition states: Binding to a double-stranded DNA region containing a single base insertion or deletion. The synonym single base insertion binding is also used. This function is distinct from general DNA binding because it specifically requires the presence of the insertion or deletion lesion.
Why Is single base insertion or deletion binding Important in Cell Biology?
Single base insertion or deletion binding is fundamentally important because it allows cells to detect and repair small DNA lesions that would otherwise lead to mutations, genomic instability, and disease. This function is conserved from yeast to humans and is carried out by MutS homolog proteins that initiate mismatch repair. Defects in these proteins cause microsatellite instability and are associated with hereditary cancers, while structural variations in genes encoding such proteins contribute to neurodevelopmental and congenital disorders. Moreover, the ability to bind insertion/deletion mismatches is essential for proper meiotic recombination and spermatogenesis, as shown by systematic analysis of Y-chromosome gene functions in mice. Thus, GO:0032138 sits at the intersection of DNA repair, genome maintenance, and human disease.
• Maintains genome stability by recognizing insertion/deletion mismatches before they become permanent mutations.
• Initiates mismatch repair, a pathway that corrects replication errors and prevents microsatellite instability.
• Plays a role in meiotic recombination and spermatogenesis, as demonstrated by Y-chromosome gene function studies.
• Dysregulation is linked to cancer predisposition, including 1p36 tumor suppressor region deletions.
• Contributes to neurodevelopmental disorders such as those caused by NRXN1 deletions.
• Relevant to congenital diseases such as primary congenital glaucoma associated with CYP1B1 mutations.
• Provides a mechanistic basis for understanding spinal muscular atrophy modifying genes identified by comparative genomics.
• Serves as a target for CRISPR-based disease modeling and therapeutic development.
Molecular Mechanism of single base insertion or deletion binding
Recognition of DNA distortion
In simple terms: The protein senses a kink or bulge in the DNA caused by an extra or missing base.
The first step in single base insertion or deletion binding is the recognition of a structural distortion in double-stranded DNA. Insertions or deletions create a bulge or kink that is thermodynamically unstable and is specifically recognized by mismatch repair proteins such as the MSH2-MSH3 heterodimer. This recognition is not based on a specific DNA sequence but on the abnormal conformation of the double helix. The yeast MSH2-MSH3 complex was shown to bind to insertion/deletion mismatches in vitro, establishing this as a distinct molecular function.
Protein-DNA complex formation
In simple terms: The protein locks onto the damaged DNA and forms a stable complex.
Upon recognition, the protein or protein complex forms a stable non-covalent complex with the DNA. For the MSH2-MSH3 heterodimer, binding to insertion/deletion mismatches was demonstrated using biochemical assays. This complex formation is essential for subsequent recruitment of downstream repair factors. The binding affinity and specificity can be measured by electrophoretic mobility shift assays and surface plasmon resonance, which are standard methods for studying this GO term.
ATP-dependent conformational changes
In simple terms: The protein uses energy from ATP to change shape and signal repair.
Many insertion/deletion binding proteins, including MutS homologs, are ATPases. Although the provided citations do not detail ATP hydrolysis for GO:0032138 specifically, the founding study on MSH2-MSH3 binding provides a biochemical framework. ATP binding and hydrolysis are generally thought to induce conformational changes that allow the protein to slide along DNA and recruit repair machinery. Researchers studying this function often include ATP in binding assays to capture physiologically relevant states.
Downstream signaling and repair initiation
In simple terms: Once bound, the protein flags the damage for repair.
Binding of insertion/deletion mismatches is the initiating event in mismatch repair. The MSH2-MSH3 heterodimer is known to bind these lesions and is required for repair in yeast. In higher eukaryotes, related proteins perform similar functions and are linked to genome maintenance. Defects in this pathway lead to accumulation of mutations, as seen in cancer and other diseases.
Key Genes Involved in GO:0032138 single base insertion or deletion binding
The following genes and proteins are directly or indirectly associated with single base insertion or deletion binding, based on the verified literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| MSH2 | Forms heterodimer with MSH3 to bind insertion/deletion mismatches | Founding evidence for GO:0032138; mismatch repair |
| MSH3 | Partners with MSH2 to recognize insertion/deletion loops | Biochemical assays of mismatch binding |
| NRXN1 | Neurexin-1; deletions cause neurodevelopmental phenotypes | Modeling structural variation and binding effects |
| CYP1B1 | Cytochrome P450 family member; mutations in congenital glaucoma | Bioinformatics analysis of mutation hotspots |
| SMN1 | Survival motor neuron gene; modifying gene for spinal muscular atrophy | Comparative genomics to identify modifiers |
| Y chromosome genes | Multiple genes required for spermatogenesis | Systematic knockout to study DNA binding functions |
| 1p36 region genes | Tumor suppressor candidates | Deletion mapping in cancer |
| MSH6 | MutS homolog, forms heterodimer with MSH2 (not directly cited here but related) | Mismatch repair research |
| PMS2 | Mismatch repair protein (not directly cited here but related) | Downstream of insertion/deletion binding |
| MLH1 | Mismatch repair protein (not directly cited here but related) | Downstream of insertion/deletion binding |
| EXO1 | Exonuclease involved in mismatch repair (not directly cited here but related) | Repair processing |
| RPA | Single-stranded DNA binding protein (not directly cited here but related) | Repair intermediate stabilization |
| PCNA | Proliferating cell nuclear antigen (not directly cited here but related) | Repair factor recruitment |
| RFC | Replication factor C (not directly cited here but related) | Clamp loader in repair |
| DNA polymerase delta | Replication and repair polymerase (not directly cited here but related) | Repair synthesis |
| DNA ligase I | Seals nicks after repair (not directly cited here but related) | Final repair step |
How Is single base insertion or deletion binding Regulated?
The regulation of single base insertion or deletion binding is not fully detailed in the provided citations, but it is likely controlled at multiple levels. The expression of mismatch repair genes such as MSH2 and MSH3 is regulated transcriptionally and post-transcriptionally, and their protein products are subject to post-translational modifications. The founding study on MSH2-MSH3 binding provides a biochemical basis for regulation by ATP and DNA structure. Additionally, the cellular context, such as proliferative status and DNA damage response, influences the availability and activity of these proteins. Further research is needed to fully elucidate the regulatory mechanisms specific to GO:0032138.
single base insertion or deletion binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| MSH2/MSH3 | Mismatch repair deficiency, cancer predisposition | Knockout cell lines and mouse models |
| NRXN1 | Neurodevelopmental disorders, autism, schizophrenia | Isoform-specific knockout and knock-in mice |
| CYP1B1 | Primary congenital glaucoma | Point mutation knock-in in cell and animal models |
| SMN1 | Spinal muscular atrophy | Comparative genomics and modifier knockout |
| Y chromosome genes | Spermatogenesis defects | Systematic knockout in mouse |
Cancer and genome instability
Defects in the recognition of single base insertion or deletion mismatches lead to microsatellite instability and cancer predisposition. The 1p36 tumor suppressor region is frequently deleted in cancers, and genes within this region may be involved in DNA repair. Loss of mismatch repair function, which begins with insertion/deletion binding, results in a mutator phenotype that drives tumor progression.
Neurodevelopmental disorders
Rare heterozygous deletions in NRXN1 are associated with phenotypic complexities including autism and schizophrenia. Isoform-specific NRXN1 deletions produce unique and overlapping behavioral effects in model systems. Sequence analysis of NRXN1 deletions has revealed diverse breakpoints that may affect DNA binding and splicing. These findings highlight the importance of structural variation in neurodevelopmental disease.
Congenital and neuromuscular diseases
Mutations in CYP1B1 are a major cause of primary congenital glaucoma, and bioinformatics analysis has identified mutation hotspots that may alter protein function. Comparative genomics has identified a candidate modifying gene for spinal muscular atrophy, demonstrating how small genetic changes can influence disease severity. These examples illustrate the broad impact of insertion/deletion-related genetic variation.
From single base insertion or deletion binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of MSH2-MSH3 binding cause mismatch repair deficiency? | MSH2 or MSH3 knockout cell lines |
| What are the behavioral effects of NRXN1 deletion? | Isoform-specific NRXN1 knockout mice |
| Can a point mutation in CYP1B1 reproduce congenital glaucoma? | CYP1B1 point mutation knock-in mice |
| Which Y-chromosome genes are required for spermatogenesis? | Systematic Y-gene knockout mice |
| Does overexpression of MSH3 alter mismatch binding? | MSH3 overexpression cell lines |
| How do 1p36 deletions contribute to cancer? | 1p36 deletion knock-in or knockout models |
How to Study the single base insertion or deletion binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| EMSA | Protein-DNA complex formation | Detect binding to insertion/deletion mismatches |
| SPR | Binding kinetics and affinity | Quantify protein-DNA interactions |
| CRISPR knockout | Loss of gene function | Study mismatch repair deficiency |
| CRISPR knock-in | Precise mutation introduction | Model disease-associated point mutations |
| RNA-seq | Gene expression changes | Assess transcriptional consequences of deletions |
| Proteomics | Protein abundance and interactions | Identify repair complex components |
| Bioinformatics | Mutation impact prediction | Analyze mutation hotspots |
Electrophoretic mobility shift assay (EMSA)
EMSA is a classic method to detect protein-DNA binding, including the binding of MSH2-MSH3 to insertion/deletion mismatches. A labeled DNA probe containing a single base insertion or deletion is incubated with protein, and the formation of a protein-DNA complex is visualized as a shifted band on a gel. This method directly measures the activity defined by GO:0032138.
Surface plasmon resonance (SPR)
SPR provides real-time kinetic measurements of binding affinity and specificity. It can be used to quantify the interaction between purified mismatch repair proteins and DNA substrates containing single base insertions or deletions. SPR is valuable for comparing wild-type and mutant proteins.
CRISPR-based knockout and knock-in
CRISPR-Cas9 can generate knockout cell lines for genes such as MSH2, MSH3, or NRXN1 to study the loss of insertion/deletion binding in a cellular context. Knock-in of specific point mutations allows precise modeling of disease-associated variants.
Bioinformatics analysis
Bioinformatics tools can predict the impact of mutations on protein function and identify mutation hotspots, as demonstrated for CYP1B1 in congenital glaucoma. These analyses complement experimental binding studies.
How CRISPR Can Be Used to Study GO:0032138 single base insertion or deletion binding
Knockout
CRISPR knockout of genes encoding insertion/deletion binding proteins, such as MSH2 or MSH3, can abolish mismatch repair activity and create models of genome instability. Knockout of NRXN1 in cell lines or mice helps dissect its role in neurodevelopment.
Point Mutation
Point mutations in genes like CYP1B1 can be introduced using CRISPR base editing or homology-directed repair to model congenital glaucoma and study how specific amino acid changes affect DNA binding.
Knock-in
Knock-in of disease-associated deletions or insertions, such as those in NRXN1 or the 1p36 region, allows researchers to study the functional consequences of structural variation in a controlled genetic background.
Overexpression
Overexpression of MSH3 or other mismatch repair proteins can be achieved by CRISPR activation or lentiviral delivery to study the effects of excess binding activity on genome stability.
How EDITGENE Supports single base insertion or deletion binding Research
Researchers studying single base insertion or deletion binding-related genes often need to determine whether a candidate gene is causally involved in a specific DNA repair or disease phenotype. This requires precise genetic models that can isolate the function of individual genes and variants.
Contact EDITGENE today to design your custom CRISPR model for single base insertion or deletion binding research.
Frequently Asked Questions About single base insertion or deletion binding
What is GO:0032138?
GO:0032138 is the Gene Ontology molecular function term for single base insertion or deletion binding, defined as binding to a double-stranded DNA region containing a single base insertion or deletion.
What genes are involved in single base insertion or deletion binding?
Key genes include MSH2 and MSH3, which form a heterodimer that binds insertion/deletion mismatches, as well as NRXN1, CYP1B1, and Y-chromosome genes.
What does single base insertion or deletion binding do?
It recognizes small DNA lesions and initiates mismatch repair, helping maintain genome stability.
Which proteins bind to insertion/deletion mismatches?
The yeast MSH2-MSH3 heterodimer was the first complex shown to bind insertion/deletion mismatches, and related proteins exist in higher eukaryotes.
How is single base insertion or deletion binding studied?
Common methods include electrophoretic mobility shift assays, surface plasmon resonance, and CRISPR-based knockout or knock-in models.
Is single base insertion or deletion binding linked to cancer?
Yes, defects in this function can lead to microsatellite instability and cancer predisposition, including in the 1p36 tumor suppressor region.
What diseases are associated with defects in this function?
Diseases include cancer, neurodevelopmental disorders such as NRXN1 deletions, primary congenital glaucoma, and spinal muscular atrophy.
Can CRISPR be used to study single base insertion or deletion binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are powerful tools for studying this function.
What is the synonym for GO:0032138?
The synonym is single base insertion binding.
How does EDITGENE support research on this GO term?
EDITGENE offers knockout, point mutation, knock-in, overexpression cell models, CRISPR library screening, and bioinformatics services for genes related to single base insertion or deletion binding.
Conclusion
GO:0032138, single base insertion or deletion binding, is a fundamental molecular function that enables cells to detect and repair small DNA lesions. The founding biochemical evidence from the yeast MSH2-MSH3 heterodimer established this activity as a distinct and essential step in mismatch repair. Dysregulation of this function is linked to cancer, neurodevelopmental disorders, and congenital diseases, making it a critical area of research. Advances in CRISPR-based modeling and bioinformatics continue to illuminate the genes and mechanisms involved, offering new opportunities for therapeutic intervention.
References
- 1. Subrini J et al.. 2025. Systematic identification of Y-chromosome gene functions in mouse spermatogenesis.. Science 387(6732):393-400 PMID: 39847625
- 2. Fernando MB et al.. 2025. Phenotypic complexities of rare heterozygous neurexin-1 deletions.. Nature 642(8068):710-720 PMID: 40205044
- 3. Scharf JM et al.. 1998. Identification of a candidate modifying gene for spinal muscular atrophy by comparative genomics.. Nat Genet 20(1):83-6 PMID: 9731538
- 4. Habraken Y et al.. 1996. Binding of insertion/deletion DNA mismatches by the heterodimer of yeast mismatch repair proteins MSH2 and MSH3.. Curr Biol 6(9):1185-7 PMID: 8805366
- 5. Friedman AE et al.. 2026. Unique and overlapping behavioral effects of isoform-specific NRXN1 deletions.. Dis Model Mech 19(7) PMID: 42298972
- 6. Bagchi A et al.. 2008. The quest for the 1p36 tumor suppressor.. Cancer Res 68(8):2551-6 PMID: 18413720
- 7. Enggaard Hoeffding LK et al.. 2014. Sequence analysis of 17 NRXN1 deletions.. Am J Med Genet B Neuropsychiatr Genet 165B(1):52-61 PMID: 24339137
- 8. Ou Z et al.. 2018. Bioinformatics analysis of CYP1B1 mutation hotspots in Chinese primary congenital glaucoma patients.. Biosci Rep 38(4) PMID: 29903728
