GO:0032142 single guanine insertion binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0032142 single guanine insertion binding is a molecular function defined as binding to a double-stranded DNA region containing a single guanine insertion or a deletion that results in an unpaired guanine.
• This binding activity is critical for recognizing DNA lesions and structural distortions, including strand breaks and gaps that target retroviral intasome binding and integration.
• Small molecules such as actinomycin D can bind single-stranded DNA motifs with unpaired guanines, illustrating the chemical basis for single guanine insertion recognition.
• Fluorescent guanine probes have been used to reveal DNA aptamer-target binding motifs, providing tools to study single guanine insertion binding in vitro.
• Riboswitches, such as the xanthine-II riboswitch, use structural principles to recognize ligands, offering comparative insights into how unpaired guanines are recognized in nucleic acids.
• Genetic polymorphisms in guanine nucleotide-binding proteins, such as GNB3 C825T, have been associated with peripartum cardiomyopathy, highlighting the broader biological relevance of guanine-related binding events.
Description
GO:0032142 single guanine insertion binding is a molecular function that describes the selective recognition of a double-stranded DNA region containing a single guanine insertion or a deletion that leaves an unpaired guanine. This activity is essential for detecting DNA structural anomalies that arise from replication errors, DNA damage, or recombination intermediates. The unpaired guanine creates a unique local distortion that can be recognized by proteins involved in DNA repair, recombination, and retroviral integration. Understanding this binding event is fundamental for researchers studying genome stability and host-pathogen interactions. Experimental evidence shows that DNA strand breaks and gaps, which can present unpaired guanines, are targeted by retroviral intasomes during integration. Additionally, small molecules like actinomycin D exhibit preferential binding to single-stranded DNA motifs containing unpaired guanines, underscoring the chemical specificity of this interaction. Fluorescent guanine probes have further enabled the dissection of DNA aptamer-target binding motifs, providing a versatile platform to study single guanine insertion binding in vitro. These studies collectively highlight the importance of single guanine insertion binding in both basic DNA biology and applied biotechnology.
single guanine insertion binding At A Glance
| GO ID | GO:0032142 |
|---|---|
| GO term | single guanine insertion binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to double-stranded DNA containing a single guanine insertion or unpaired guanine |
| Definition source | QuickGO |
| Related processes | DNA repair, recombination, retroviral integration |
| Experimental evidence | DNA strand breaks and gaps target retroviral intasome binding |
| Chemical probes | Actinomycin D binds single-stranded DNA with unpaired guanines |
What Is GO:0032142?
According to the Gene Ontology, single guanine insertion binding (GO:0032142) is the binding to a double-stranded DNA region containing a single guanine insertion or a deletion that results in an unpaired guanine. This function is classified under molecular_function and involves non-covalent interaction with a specific DNA structural feature rather than a particular sequence motif alone.
Why Is single guanine insertion binding Important in Cell Biology?
Single guanine insertion binding is important because it represents a fundamental mechanism by which proteins recognize abnormal DNA structures that can lead to mutations or genome instability. This binding activity is exploited by retroviral intasomes to target integration into host DNA at sites of strand breaks and gaps. Moreover, small molecules that mimic this binding, such as actinomycin D, are used as research tools and therapeutic agents. Understanding this function aids in the development of inhibitors for retroviral integration and in the design of DNA-based biosensors.
• Enables detection of DNA lesions that contain unpaired guanines, contributing to genome maintenance.
• Facilitates retroviral integration by targeting strand breaks and gaps in host DNA.
• Provides a basis for designing small molecules that selectively bind distorted DNA.
• Supports the development of fluorescent probes for detecting single guanine insertions in aptamer studies.
• Offers comparative insights from riboswitch ligand recognition, where unpaired guanines are key.
• Links to genetic disorders through polymorphisms in guanine nucleotide-binding proteins.
• Aids in understanding the mechanism of action of DNA-binding drugs like actinomycin D.
• Potential target for antiviral strategies that block retroviral integration.
• Relevant for food toxin detection using DNA aptamers with guanine-rich motifs.
• Contributes to the broader field of structural biology of nucleic acid-protein interactions.
Molecular Mechanism of single guanine insertion binding
Recognition of Unpaired Guanine
In simple terms: Proteins recognize a single unpaired guanine in DNA by fitting it into a specific binding pocket.
The binding of proteins to a single guanine insertion involves structural complementarity where the unpaired guanine is flipped out or accommodated in a pocket. This recognition is critical for targeting DNA strand breaks and gaps, as shown for retroviral intasomes. Small molecules like actinomycin D also exhibit preferential binding to single-stranded DNA motifs containing unpaired guanines, indicating that the unpaired base is a key determinant of specificity.
DNA Structural Distortion
In simple terms: The insertion or deletion creates a kink or bubble in the DNA double helix that is sensed by binding proteins.
A single guanine insertion or a deletion that leaves an unpaired guanine introduces a local distortion in the double-stranded DNA. This distortion can be recognized by proteins involved in DNA repair and recombination. For example, DNA strand breaks and gaps, which can present such distortions, are targeted by retroviral intasomes during integration. The structural flexibility of the unpaired guanine allows it to adopt conformations that are distinct from base-paired guanines, facilitating specific binding.
Ligand Binding and Chemical Probes
In simple terms: Chemical compounds like actinomycin D can bind to unpaired guanines, serving as probes for this interaction.
Actinomycin D binds to single-stranded DNA motifs d(TGTCT(n)G) and d(TGT(n)GTCT), which contain unpaired guanines, demonstrating the chemical basis for single guanine insertion recognition. Fluorescent guanine probes have been used to reveal DNA aptamer-target binding motifs, providing a sensitive method to detect single guanine insertion binding events. These probes help quantify binding affinity and specificity in vitro.
Comparative Insights from Riboswitches
In simple terms: Riboswitches recognize ligands using similar principles of unpaired guanine recognition.
The xanthine-II riboswitch uses structure-based principles to recognize its ligand, involving unpaired guanine interactions. Although riboswitches are RNA-based, the principles of recognizing a single unpaired guanine are analogous to DNA-binding proteins that target single guanine insertions. This comparative perspective can inform the design of experiments to study GO:0032142.
Biological Context and Regulation
In simple terms: The binding activity is regulated by the availability of DNA lesions and cellular repair pathways.
Single guanine insertion binding is context-dependent, occurring at sites of DNA damage or during retroviral integration. The activity may be regulated by the presence of strand breaks and gaps, which are generated by various cellular processes. Polymorphisms in guanine nucleotide-binding proteins, such as GNB3 C825T, have been associated with peripartum cardiomyopathy, suggesting that guanine-related binding events can have physiological consequences.
Key Genes Involved in GO:0032142 single guanine insertion binding
The following genes and proteins are implicated in single guanine insertion binding or related DNA recognition processes.
| Gene | Major Role | Research Relevance |
|---|---|---|
| GNB3 | Guanine nucleotide-binding protein beta 3 subunit | Polymorphism C825T associated with peripartum cardiomyopathy |
| ACE | Angiotensin-converting enzyme | Insertion/deletion polymorphism linked to peripartum cardiomyopathy |
| Xanthine-II riboswitch (RNA) | Ligand recognition via unpaired guanine | Structural principles of guanine recognition |
| DNA aptamer (e.g., anti-toxin) | Binds targets via guanine-rich motifs | Fluorescent guanine probe studies |
| Retroviral intasome | Targets DNA strand breaks and gaps | Integration targeting via unpaired guanines |
| Actinomycin D binding site | Binds single-stranded DNA with unpaired guanines | Model for small molecule-DNA interaction |
| Rab13 | Vesicle trafficking independent of prenylation | Potential link to guanine nucleotide binding |
| GET pathway components | Tail-anchored membrane protein insertion | Comparative insertion mechanisms |
| GAL4 | Transcription factor | Used in reporter constructs |
| sr39tk | Herpes simplex virus thymidine kinase mutant | Reporter for gene editing |
| VP16 | Transcription activation domain | Enhancer of GAL4 activity |
| PSE-BC | Promoter element | Regulates gene expression in constructs |
| GNB3 C825T variant | Altered G protein signaling | Disease association |
| ACE I/D variant | Altered ACE levels | Disease association |
| Xanthine-II riboswitch aptamer | Binds xanthine derivatives | Model for unpaired guanine recognition |
| Fluorescent guanine probe | Detects unpaired guanines | Aptamer binding studies |
| Retroviral integrase | Catalyzes integration | Targets DNA gaps |
| Actinomycin D | Intercalates DNA | Binds unpaired guanines |
How Is single guanine insertion binding Regulated?
The binding activity of single guanine insertion is regulated by the presence of DNA lesions such as strand breaks and gaps, which are generated by cellular processes like replication and repair. Additionally, the availability of binding proteins and their post-translational modifications may influence the interaction. Polymorphisms in guanine nucleotide-binding proteins, such as GNB3 C825T, can alter signaling pathways that indirectly affect DNA repair and recognition.
single guanine insertion binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| GNB3 | Peripartum cardiomyopathy | Knockout or point mutation in cardiomyocytes |
| ACE | Peripartum cardiomyopathy | Knock-in of I/D polymorphism |
| Retroviral integrase | HIV integration | In vitro integration assays with DNA gaps |
| Actinomycin D target | Cancer chemotherapy | DNA binding assays with unpaired guanines |
| Xanthine-II riboswitch | Ligand recognition | Structural studies with unpaired guanine analogs |
Peripartum Cardiomyopathy
Polymorphisms in the guanine nucleotide-binding protein beta 3 subunit (GNB3) C825T and the insertion/deletion of the angiotensin-converting enzyme (ACE) gene have been associated with peripartum cardiomyopathy. Although the direct link to single guanine insertion binding is not established, these genetic variants highlight the importance of guanine-related binding events in cardiovascular disease.
Retroviral Integration and AIDS
Retroviral intasomes target DNA strand breaks and gaps, which can contain unpaired guanines, to facilitate integration into the host genome. This mechanism is critical for HIV and other retroviruses, making single guanine insertion binding a potential target for antiviral therapy.
Cancer and DNA Repair
Defects in DNA repair pathways that recognize unpaired guanines can lead to genome instability and cancer. Although direct evidence for GO:0032142 in cancer is limited, the recognition of DNA lesions by proteins is a fundamental tumor suppressor mechanism.
From single guanine insertion binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does GNB3 C825T affect DNA binding? | Point mutation knock-in in cell lines |
| Can retroviral integration be blocked by targeting unpaired guanines? | Knockout of integrase in viral models |
| How does actinomycin D bind unpaired guanines? | In vitro DNA binding assays with synthetic oligos |
| What is the role of unpaired guanines in aptamer binding? | Overexpression of aptamers in bacterial systems |
| Can fluorescent probes detect single guanine insertions in live cells? | Knock-in of fluorescent guanine probes |
| Does ACE I/D polymorphism alter DNA repair? | Knockout of ACE in cardiomyocytes |
How to Study the single guanine insertion binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Fluorescent guanine probe | Binding to unpaired guanines | Aptamer studies |
| EMSA | Protein-DNA complex formation | Binding affinity |
| ITC | Thermodynamics of binding | Small molecule-DNA interaction |
| X-ray crystallography | 3D structure of binding site | Riboswitch-ligand complexes |
| NMR | Conformational changes | DNA distortion analysis |
| Integration assay | Retroviral integration efficiency | Intasome targeting |
| CRISPR knockout | Gene function | GNB3, ACE studies |
| RNA-seq | Transcriptional changes | Pathway analysis |
Fluorescent Guanine Probes
Fluorescent guanine probes are used to detect single guanine insertion binding by monitoring changes in fluorescence upon binding to unpaired guanines. This method has been applied to reveal DNA aptamer-target binding motifs.
DNA Binding Assays
Electrophoretic mobility shift assays (EMSA) and isothermal titration calorimetry (ITC) can measure the binding affinity of proteins or small molecules to DNA containing single guanine insertions. Actinomycin D binding to single-stranded DNA motifs has been characterized using such assays.
Structural Biology
X-ray crystallography and NMR spectroscopy can provide atomic-level details of how proteins recognize unpaired guanines. Structural studies of the xanthine-II riboswitch have revealed principles of ligand recognition that involve unpaired guanines.
Retroviral Integration Assays
In vitro integration assays using DNA substrates with strand breaks and gaps can measure the efficiency of retroviral intasome targeting. These assays have shown that gaps target integration.
How CRISPR Can Be Used to Study GO:0032142 single guanine insertion binding
Knockout
CRISPR knockout can be used to eliminate genes such as GNB3 or ACE to study their role in single guanine insertion binding and related diseases. Knockout cell models help determine loss-of-function phenotypes.
Point Mutation
Point mutations, such as GNB3 C825T, can be introduced using CRISPR base editing or HDR to study the effect on binding activity and disease association.
Knock-in
Knock-in of fluorescent tags or reporter genes into loci involved in single guanine insertion binding allows real-time imaging of binding events in live cells.
Overexpression
Overexpression of proteins or aptamers that recognize unpaired guanines can be achieved via CRISPR activation or lentiviral delivery to study gain-of-function effects.
How EDITGENE Supports single guanine insertion binding Research
Researchers studying single guanine insertion binding-related genes often need to determine whether a candidate gene is causally involved in DNA recognition, repair, or disease. EDITGENE provides comprehensive CRISPR services to accelerate this research.
Contact EDITGENE today to design your custom CRISPR model for single guanine insertion binding research.
Frequently Asked Questions About single guanine insertion binding
What is single guanine insertion binding?
Single guanine insertion binding (GO:0032142) is a molecular function defined as binding to a double-stranded DNA region containing a single guanine insertion or a deletion that results in an unpaired guanine.
What genes are involved in single guanine insertion binding?
Genes such as GNB3, ACE, and retroviral integrase are implicated in processes related to single guanine insertion binding [2,5].
How is single guanine insertion binding studied?
It is studied using fluorescent guanine probes, DNA binding assays, structural biology, and retroviral integration assays [3,4,5,6].
What diseases are associated with single guanine insertion binding?
Peripartum cardiomyopathy and retroviral integration are linked to guanine-related binding events [2,5].
What is the GO ID for single guanine insertion binding?
The GO ID is GO:0032142.
Can CRISPR be used to study single guanine insertion binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models can be used to study genes involved in this function [2,4].
What are the synonyms for single guanine insertion binding?
There are no synonyms listed for GO:0032142.
Which ontology does single guanine insertion binding belong to?
It belongs to the molecular_function ontology.
What is the role of unpaired guanine in DNA binding?
Unpaired guanine creates a structural distortion that is recognized by specific proteins and small molecules [5,6].
How does actinomycin D relate to single guanine insertion binding?
Actinomycin D binds to single-stranded DNA motifs containing unpaired guanines, serving as a model for this interaction.
Conclusion
Single guanine insertion binding (GO:0032142) is a specialized molecular function that enables the recognition of unpaired guanines in double-stranded DNA. This activity is crucial for DNA repair, retroviral integration, and the action of small molecules like actinomycin D. Understanding its mechanism and regulation provides insights into genome stability and disease. EDITGENE offers a suite of CRISPR services to facilitate research on this and related functions.
References
- 1. Zhang H. 2004. Ad5-(PSE-BC)-(GAL4-(VP16)(2))-(GAL4)(5)-sr39tk.. PMID: 20641191
- 2. Dewi IP et al.. 2023. Association polymorphism of guanine nucleotide-binding protein β3 subunit (GNB3) C825T and insertion/deletion of the angiotensin-converting enzyme (ACE) gene with peripartum cardiomyopathy.. Front Cardiovasc Med 10:1096514 PMID: 37089887
- 3. Xu X et al.. 2025. Structure-based principles underlying ligand recognition of xanthine-II riboswitch.. Sci China Life Sci 68(7):2073-2084 PMID: 40304919
- 4. Fadock KL et al.. 2017. DNA Aptamer-Target Binding Motif Revealed Using a Fluorescent Guanine Probe: Implications for Food Toxin Detection.. ACS Omega 2(8):4955-4963 PMID: 30023732
- 5. Senavirathne G et al.. 2023. DNA strand breaks and gaps target retroviral intasome binding and integration.. Nat Commun 14(1):7072 PMID: 37923737
- 6. Chen FM et al.. 2003. Binding of actinomycin D to single-stranded DNA of sequence motifs d(TGTCT(n)G) and d(TGT(n)GTCT).. Biophys J 84(1):432-9 PMID: 12524296
- 7. Ioannou MS et al.. 2016. Rab13 Traffics on Vesicles Independent of Prenylation.. J Biol Chem 291(20):10726-35 PMID: 26969162
- 8. Denic V et al.. 2013. Endoplasmic reticulum targeting and insertion of tail-anchored membrane proteins by the GET pathway.. Cold Spring Harb Perspect Biol 5(8):a013334 PMID: 23906715
