DDB2 is a 48 kDa subunit of the UV-DDB heterodimer (DDB1-DDB2), which binds cyclobutane pyrimidine dimers (CPDs) and other DNA lesions. This complex interacts with CUL4A and ROC1 to polyubiquitinate targets, facilitating NER (1, 4, 8). Mutations in DDB2 cause XP complementation group E, characterized by UV sensitivity, skin cancer, and neurological defects (1, 4, 8).
Recombinant monoclonal antibodies (rMAbs) are produced via engineered expression systems, offering advantages over traditional methods:
Feature | Recombinant rMAbs | Traditional MAbs |
---|---|---|
Production | Defined genetic sequences, batch consistency | Hybridoma-dependent, variable |
Specificity | Engineered binding regions for affinity | Limited epitope targeting |
Cross-reactivity | Controlled via sequence design | Higher risk of off-target binding |
Applications | Therapeutic/diagnostic engineering | Primarily research use |
DDB2 rMAbs are validated for:
Application | Dilution Range | Key Findings |
---|---|---|
Western Blot | 1:500–1:2000 | Detects 48–51 kDa bands in HeLa, A431, and mouse kidney/liver lysates (3, 9, 11) |
Immunofluorescence | 1:50–1:200 | Localizes DDB2 to nuclear regions, colocalizing with UV-induced DNA damage (3, 11) |
ELISA | Varies | Quantifies DDB2 levels in cell lysates or tissue extracts (5, 9) |
Immunoprecipitation | N/A | Identifies DDB2 interactions with CUL4A and ROC1 (4, 8) |
UV-DDB Complex Role: DDB2 rMAbs confirm the complex’s recruitment to CPDs, initiating NER. Deficiency correlates with XP-E pathology (1, 4, 8).
Cancer Research: DDB2 overexpression is linked to oncogenic roles in breast cancer, suppressing SOD2 and promoting cell growth (9, 11).
CUL4A-ROC1 Ubiquitination: DDB2 antibodies validate the UV-DDB complex’s interaction with CUL4A, enabling ubiquitination of XPC (4, 8).
HBV X Protein: DDB2 may mediate viral transactivation via DDB1 interaction, though direct evidence remains limited (1, 8).
This DDB2 recombinant monoclonal antibody is produced using in vitro expression systems. The antibody's DNA sequences are cloned from immunoreactive rabbits, and the immunogen used is a synthetic peptide derived from the human DDB2 protein. These antibody-encoding genes are then inserted into plasmid vectors and transfected into host cells for antibody expression. The purified recombinant monoclonal antibody is rigorously tested in ELISA, WB, IHC, and FC applications to confirm its reactivity with the human DDB2 protein.
DDB2 is a DNA damage recognition protein playing a critical role in the nucleotide excision repair (NER) pathway. The NER pathway identifies and repairs various DNA lesions, particularly those caused by UV radiation. DDB2's function in DNA repair maintains genomic integrity and prevents mutations that can lead to cancer and other diseases.
DDB2, a protein involved in both DNA repair and protein ubiquitination, functions as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively.
As a core component of the UV-DDB complex (UV-damaged DNA-binding protein complex), DDB2 recognizes UV-induced DNA damage and recruits proteins from the NER pathway to initiate DNA repair. The UV-DDB complex demonstrates a preference for binding to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites, and short mismatches.
DDB2 also functions as the substrate recognition module for the DCX (DDB2-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB2-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB2-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3, and histone H4 at sites of UV-induced DNA damage. This ubiquitination facilitates histone removal from the nucleosome and promotes subsequent DNA repair.
The DDB2-CUL4-ROC1 complex also ubiquitinates XPC, potentially enhancing DNA-binding by XPC and promoting NER. Additionally, the complex ubiquitinates KAT7/HBO1 in response to DNA damage, leading to its degradation. This recognition of KAT7/HBO1 follows phosphorylation by ATR.
DDB2 exhibits inhibitory effects on UV-damaged DNA repair.
DDB2 is a 427 amino acid protein containing seven WD repeats that belongs to the WD repeat DDB2/WDR76 family. It localizes in the nucleus and plays critical roles in DNA repair mechanisms. DDB2 is particularly significant in research because it negatively regulates the constitutive expression of the SOD2 gene in breast cancer cells and may function as an oncogene. Its potential role as a predictive marker in breast cancer makes it an important target for antibody-based research applications .
The protein has a calculated molecular weight of approximately 48 kDa, with observed molecular weights typically ranging between 47-51 kDa in Western blot applications . Understanding DDB2's function is essential for researchers studying DNA damage repair pathways, UV damage responses, and cancer development mechanisms.
DDB2 recombinant monoclonal antibodies have been validated for multiple research applications:
When designing experiments, researchers should optimize antibody dilutions for their specific experimental conditions, as the recommended ranges provide starting points but may require adjustment based on sample type, detection method, and target expression level .
Proper storage is critical for maintaining antibody activity. Most DDB2 recombinant monoclonal antibodies should be stored at -20°C or -80°C for long-term preservation . For short-term storage and frequent use, 4°C is acceptable for up to one month . Most manufacturers supply the antibodies in a stabilizing buffer containing components such as:
Phosphate buffered saline (PBS)
0.02% sodium azide
50% glycerol
The glycerol prevents freezing at -20°C and reduces damage from freeze-thaw cycles. To maximize antibody shelf-life and activity:
Avoid repeated freeze-thaw cycles
Consider aliquoting the antibody upon receipt
Thaw frozen antibodies completely before use
Following these storage guidelines will ensure consistent results and extend the usable life of the antibody preparation.
Validating antibody specificity is crucial for generating reliable research data. For DDB2 recombinant monoclonal antibodies, implement this multifaceted validation approach:
Positive and negative controls: Use cell lines with known DDB2 expression levels. PC-3, A431, HCT 116, HeLa, HepG2, and Jurkat cells have been demonstrated to express DDB2 and can serve as positive controls . Consider using DDB2-knockout cell lines as negative controls.
Western blot analysis: Verify a single band at the expected molecular weight (47-51 kDa). Multiple bands may indicate non-specific binding or protein degradation .
Peptide competition assay: Pre-incubate the antibody with the immunizing peptide before application. This should abolish specific signal if the antibody is truly specific.
Knockdown verification: Compare staining in wild-type cells versus cells subjected to DDB2 siRNA knockdown or CRISPR/Cas9 knockout. The signal should significantly decrease in knockdown/knockout cells.
Cross-species reactivity testing: If your research involves multiple species, verify reactivity with each species individually. Many DDB2 antibodies react with human, mouse, and rat DDB2, but cross-reactivity should be experimentally confirmed .
Immunoprecipitation-mass spectrometry: For definitive validation, perform IP with the antibody followed by mass spectrometry to confirm that DDB2 is the predominant protein being pulled down.
Comprehensive validation ensures that experimental findings can be attributed to DDB2 with high confidence.
Western blot optimization for DDB2 detection requires attention to several critical factors:
Sample preparation:
Blocking conditions:
5% non-fat dry milk or 3-5% BSA in TBST typically works well
Optimize blocking time (1-2 hours at room temperature or overnight at 4°C)
Antibody dilution:
Incubation conditions:
Primary: Overnight at 4°C often yields cleaner results than shorter incubations at room temperature
Secondary: 1-2 hours at room temperature is typically sufficient
Washing stringency:
Increase number and duration of washes if background is high
TBST (TBS with 0.1% Tween-20) is commonly used
Detection system selection:
Choose based on expected expression levels (chemiluminescence, fluorescence)
Enhanced chemiluminescence systems work well for most DDB2 detection applications
Expected results:
Detailed optimization records should be maintained to ensure reproducibility across experiments.
Effective immunohistochemistry (IHC) with DDB2 recombinant monoclonal antibodies requires careful methodology:
Tissue fixation and processing:
Formalin-fixed, paraffin-embedded (FFPE) tissues are commonly used
Consider fixation time's effect on antigen preservation
Optimal sectioning thickness is typically 4-6 μm
Antigen retrieval methods:
Blocking parameters:
Antibody dilution and incubation:
Detection systems:
Controls and interpretation:
Multiplex considerations:
For co-localization studies, select antibodies raised in different species
Use appropriate fluorophore combinations if implementing multiplex fluorescent IHC
These methodological considerations will help ensure specific and reproducible DDB2 detection in tissue samples.
Recombinant monoclonal antibodies represent a significant advancement over traditional antibody technologies, with several key advantages for DDB2 research:
For DDB2 research applications requiring high precision, such as quantitative analysis of protein levels across multiple experiments or laboratories, recombinant monoclonal antibodies provide superior consistency and reliability . The defined nature of the binding site also enables more precise epitope mapping and functional studies.
The fixed sequence of recombinant antibodies eliminates concerns about genetic drift that can occur in hybridoma cell lines over time, ensuring that experimental results remain comparable throughout a research project's duration .
Resolving conflicting results with different DDB2 antibodies requires systematic troubleshooting and validation:
Epitope mapping comparison:
Post-translational modification interference:
Determine if phosphorylation, ubiquitination, or other modifications may block epitope recognition
Consider using phosphatase treatment or other modification-removing approaches to standardize samples
Cross-reactivity analysis:
Test antibodies against recombinant DDB2 protein and closely related family members
Perform immunoprecipitation followed by mass spectrometry to identify all proteins being recognized
Antibody validation across multiple techniques:
If antibody A works in WB but not IHC while antibody B shows the reverse pattern, use complementary approaches
Consider chromatin immunoprecipitation (ChIP) to validate DNA-binding capacity
Implement proximity ligation assays to confirm protein-protein interactions
Knockout/knockdown controls with multiple antibodies:
Generate DDB2 knockout or knockdown models
Test all antibodies against these negative controls
Antibodies showing signal in knockout models may have specificity issues
Experimental condition standardization:
Develop a unified protocol that works across antibodies
Standardize fixation, antigen retrieval, and detection methods
Consider native versus denatured conditions' impact on epitope accessibility
Collaborative validation:
Partner with other laboratories to verify findings
Implement round-robin testing using standardized samples and protocols
When reporting results, transparently document which antibody was used and its validation parameters to enable proper interpretation of the findings.
DDB2 recombinant monoclonal antibodies provide powerful tools for investigating DDB2's role in cancer pathways through multiple experimental approaches:
Expression profiling across cancer types:
Mechanistic studies of DNA repair deficiencies:
Implement immunofluorescence co-localization with γH2AX to assess DDB2 recruitment to DNA damage sites
Quantify repair kinetics through time-course experiments after UV damage
Compare repair efficiency in DDB2-high versus DDB2-low cancer cell populations
Chromatin dynamics and transcriptional regulation:
Protein-protein interaction networks:
Use antibodies for co-immunoprecipitation to identify DDB2 binding partners
Implement proximity ligation assays to confirm interactions in situ
Analyze how these interactions change during cancer progression
Cell cycle and proliferation regulation:
Combine DDB2 staining with cell cycle markers in flow cytometry
Assess correlation between DDB2 levels and proliferation rates
Investigate checkpoint activation in response to DNA damage
Therapeutic response prediction:
Stratify patient-derived xenografts by DDB2 expression
Correlate expression with response to DNA-damaging therapies
Develop companion diagnostic approaches for treatment selection
Post-translational modification profiling:
Use phospho-specific or ubiquitin-specific DDB2 antibodies
Map modifications in response to therapy
Correlate modification patterns with treatment resistance
These approaches can help elucidate DDB2's multifaceted roles in cancer, potentially identifying new therapeutic targets and diagnostic markers.
Understanding and mitigating false results is essential for reliable DDB2 research:
False Positive Causes and Solutions:
Cross-reactivity with related proteins:
Non-specific binding to abundant proteins:
Issue: Particularly problematic in high-expression tissues
Solution: Optimize blocking conditions and increase washing stringency
Implementation: Test different blocking agents (BSA, normal serum, commercial blockers)
Secondary antibody cross-reactivity:
Issue: Secondary antibodies may recognize endogenous immunoglobulins
Solution: Include secondary-only controls and consider using directly conjugated primaries
Implementation: Pre-adsorb secondary antibodies against tissue lysates
Endogenous peroxidase or phosphatase activity:
Issue: Creates false signal in enzyme-based detection systems
Solution: Include appropriate blocking steps
Implementation: Treat samples with hydrogen peroxide (for HRP) or levamisole (for alkaline phosphatase)
False Negative Causes and Solutions:
Epitope masking by fixation:
Low expression levels:
Issue: DDB2 expression varies by tissue and condition
Solution: Use signal amplification systems and optimize detection sensitivity
Implementation: Try tyramide signal amplification or more sensitive detection reagents
Post-translational modifications:
Protein degradation:
Issue: Nuclear proteins can degrade rapidly after sample collection
Solution: Minimize processing time and include protease inhibitors
Implementation: Use fresh samples when possible and process consistently
Antibody degradation:
Systematic controls and thorough validation are essential for distinguishing true results from artifacts.
Comparing DDB2 expression across varied samples requires careful methodological standardization:
Sample preparation standardization:
Tissue collection: Standardize collection time, fixation duration, and processing protocols
Cell culture: Harvest at consistent confluence and cell cycle stage
Protein extraction: Use identical lysis buffers and extraction methods
Control for nuclear versus whole-cell fractionation differences
Normalization strategies:
Western blot:
Load equal total protein (validated by total protein stains like Ponceau S)
Normalize to multiple housekeeping proteins (e.g., β-actin plus GAPDH)
Consider nuclear-specific loading controls for nuclear proteins like DDB2
IHC/IF:
Use ratio to nuclear stain intensity
Include calibration standards on each slide
Process all samples in a single batch when possible
Quantification methods:
Western blot: Use linear range of detection for densitometry
IHC: Implement digital pathology scoring rather than subjective assessment
Flow cytometry: Use calibration beads to standardize fluorescence intensity
Technical and biological replicates:
Perform at minimum three technical replicates
Include biological replicates appropriate to sample type
Calculate and report statistical confidence intervals
Controls and reference standards:
Multi-method validation:
Confirm key findings with orthogonal techniques
Compare protein expression (Western blot) with mRNA levels (qPCR)
Validate subcellular localization (IF) with fractionation (Western blot)
Data reporting standards:
Present raw data alongside normalized results
Clearly document all normalization calculations
Report statistical methods used for comparisons
By implementing these standardized approaches, researchers can generate robust comparative data on DDB2 expression that minimizes technical variation and highlights true biological differences.
Flow cytometry applications with DDB2 recombinant monoclonal antibodies require specific methodological considerations:
Cell preparation optimization:
Nuclear protein detection challenges:
DDB2 is predominantly nuclear, requiring effective nuclear permeabilization
Balance permeabilization strength with cellular integrity
Consider specialized nuclear protein staining kits
Validate protocol with known nuclear markers
Antibody titration and controls:
Multiparameter analysis design:
For cell cycle analysis: Combine DDB2 with DNA content dye (PI, DAPI)
For DNA damage studies: Include γH2AX or 53BP1 markers
For apoptosis correlation: Add Annexin V and caspase activation markers
Select fluorophores with minimal spectral overlap
Signal amplification considerations:
Primary-secondary antibody approach may enhance sensitivity
Biotin-streptavidin systems can amplify dim signals
Tyramide signal amplification for very low abundance detection
Balance amplification with background increase
DDB2 dynamics after DNA damage:
Include time-course analysis after UV or chemical damage
Standardize damage induction protocols
Coordinate fixation timing precisely across samples
Consider live-cell options with fluorescently tagged DDB2 constructs
Data analysis approaches:
Gating strategy: Define positive populations based on controls
Quantification: Mean fluorescence intensity and percent positive cells
Bivariate analysis: DDB2 levels versus cell cycle phase
Statistical evaluation of population shifts
Example protocol framework:
Harvest cells in single-cell suspension
Fix with 4% formaldehyde for 15 minutes at room temperature
Permeabilize with 0.1% Triton X-100 for 10 minutes
Block with 3% BSA for 30 minutes
Incubate with DDB2 antibody (1:100 dilution) for 1 hour at room temperature
Wash 3× with PBS containing 0.1% Tween-20
Incubate with fluorophore-conjugated secondary antibody for 30 minutes
Wash 3× with PBS containing 0.1% Tween-20
Counterstain DNA with appropriate dye
Analyze on flow cytometer with appropriate laser/filter configuration
This optimized methodology enables accurate assessment of DDB2 dynamics in relation to cell cycle progression and DNA damage responses.
DDB2 recombinant monoclonal antibodies offer powerful tools for high-throughput screening (HTS) of compounds affecting DNA damage response pathways:
Automated imaging platforms:
Implement immunofluorescence-based detection of DDB2 nuclear localization
Quantify recruitment to DNA damage sites after UV microirradiation
Measure co-localization with other repair factors (XPC, PCNA)
Use 96/384-well formats compatible with automated microscopy
Flow cytometry-based HTS adaptations:
Develop protocols for fixed-cell detection of DDB2 in microplate formats
Combine with DNA content and damage markers
Implement machine learning algorithms for complex phenotype recognition
Screen for compounds that modulate DDB2 expression or localization
ELISA-based quantification approaches:
Develop sandwich ELISA systems using DDB2 recombinant antibodies
Measure total DDB2 levels across treatment conditions
Detect specific post-translational modifications
Implement in 384-well formats for higher throughput
Protein-protein interaction screening:
Adapt proximity ligation assays for DDB2 interactome analysis
Screen for compounds disrupting key interactions
Combine with split-reporter systems (BRET, FRET) for live-cell monitoring
Focus on DDB2-XPC or DDB2-CUL4A interactions as therapeutic targets
Reporter cell line development:
Create cell lines expressing fluorescently tagged DDB2
Monitor real-time dynamics after compound treatment
Implement CRISPR-edited endogenous tagging for physiological expression
Validate with recombinant antibodies before large-scale screening
Multiplexed detection strategies:
Combine DDB2 detection with other DNA repair markers
Implement CyTOF (mass cytometry) for higher-dimensional analysis
Use barcoding strategies for increased throughput
Develop algorithms to identify complex repair phenotypes
Data integration approaches:
Connect DDB2 dynamics data with transcriptomic changes
Correlate with cell survival and genomic stability metrics
Implement machine learning for predictive biomarker identification
Develop pathway-focused analysis algorithms
These approaches could accelerate the discovery of compounds that modulate DDB2 function, potentially leading to novel therapeutics for cancer and other diseases related to DNA repair deficiencies.
Developing phospho-specific DDB2 antibodies presents unique challenges requiring specialized approaches:
Key phosphorylation sites identification:
Challenge: DDB2 has multiple potential phosphorylation sites
Solution: Use mass spectrometry to identify functionally relevant sites
Implementation: Perform phosphoproteomic analysis before and after DNA damage
Focus on sites with demonstrated functional significance (e.g., those affecting protein-protein interactions or DNA binding)
Phosphopeptide immunogen design:
Challenge: Ensuring site-specificity and minimizing cross-reactivity
Solution: Careful phosphopeptide design with flanking sequences
Implementation: Include 7-15 amino acids surrounding the phosphorylation site
Consider multiple immunogen designs with different carrier proteins
Recombinant antibody development advantages:
Challenge: Traditional hybridoma methods often yield antibodies with suboptimal specificity
Solution: Use phage or yeast display platforms for direct selection
Implementation: Select antibodies using both phosphorylated and non-phosphorylated peptides
Implement negative selection steps against similar phosphopeptides
Rigorous specificity validation:
Challenge: Confirming absolute phospho-specificity
Solution: Comprehensive validation using multiple approaches
Implementation:
Test against phosphatase-treated samples
Use phospho-null mutants (Ser/Thr → Ala)
Employ competing peptide studies
Validate with phosphorylation-inducing stimuli
Temporal dynamics characterization:
Challenge: Phosphorylation events may be transient
Solution: Develop time-course protocols with phosphatase inhibitors
Implementation: Optimize sample collection timing after stimuli
Use combinatorial inhibitor strategies to maximize phospho-signal
Low abundance detection:
Challenge: Phosphorylated forms may represent a small fraction of total DDB2
Solution: Develop enrichment strategies before detection
Implementation:
Phosphoprotein enrichment columns
Immunoprecipitation with total DDB2 antibodies before phospho-detection
Signal amplification methods for IHC/IF applications
Validation across multiple applications:
Challenge: Epitope accessibility varies by technique
Solution: Optimize for each application separately
Implementation:
WB: Optimize transfer conditions and blocking
IHC: Develop specific antigen retrieval protocols
IF: Test multiple fixation and permeabilization methods
Example validation data table for phospho-DDB2 antibodies:
Validation Method | Expected Result | Interpretation |
---|---|---|
Lambda phosphatase treatment | Signal elimination | Confirms phospho-specificity |
Phospho-null mutation (S→A) | Signal elimination | Confirms site-specificity |
Phospho-mimetic (S→E) | No detection | Confirms true phospho-recognition |
UV damage time course | Signal increase | Confirms biological relevance |
ATR/ATM inhibitor pretreatment | Signal reduction | Validates pathway involvement |
Competition with phos-peptide | Signal elimination | Confirms epitope specificity |
Competition with non-phos peptide | No effect | Confirms phospho-requirement |
These methodological considerations and validation strategies are essential for developing reliable phospho-specific DDB2 antibodies that can advance understanding of DDB2 regulation in DNA damage responses.
DDB2 recombinant monoclonal antibodies hold significant potential for advancing precision medicine in cancer:
Biomarker development for treatment stratification:
DDB2 expression levels correlate with DNA repair capacity
Antibody-based tissue analysis can predict response to DNA-damaging therapies
Potential applications in selecting patients for platinum agents, PARP inhibitors, or radiotherapy
DDB2's reported role as an oncogene in breast cancer suggests potential as a predictive marker
Companion diagnostic development:
Standardized IHC assays using recombinant antibodies
Quantitative scoring systems for therapy selection
Multiplexed approaches combining DDB2 with other DNA repair markers
Digital pathology integration for objective assessment
Monitoring therapy response:
Serial liquid biopsy analysis of circulating tumor cells
DDB2 expression changes as pharmacodynamic markers
Correlation with circulating tumor DNA levels
Real-time adjustment of treatment regimens
Tumor heterogeneity assessment:
Spatial analysis of DDB2 expression within tumors
Identification of therapy-resistant subpopulations
Guidance for combination therapy approaches
Integration with single-cell analysis technologies
Emerging immunotherapeutic connections:
DDB2's potential role in regulating tumor immunogenicity
Correlation with tumor mutational burden
Antibody-based assessment of DDB2 in immune cells
Potential biomarker for immunotherapy response
Functional testing platforms:
Patient-derived organoid testing with DDB2 assessment
Ex vivo drug sensitivity correlation with DDB2 levels
Development of functional biomarker assays
Personalized therapy selection based on DDB2 pathway activity
Clinical decision support development:
Integration of DDB2 testing into treatment algorithms
Machine learning models incorporating DDB2 with other biomarkers
Electronic health record integration
Clinical trial stratification based on DDB2 status
Clinical implementation considerations:
Analytical validation of antibody performance across laboratories
Clinical validation in retrospective and prospective studies
Standardization of testing protocols
Regulatory approval pathways for diagnostic applications
The superior consistency, specificity, and reproducibility of recombinant monoclonal antibodies make them particularly suitable for clinical diagnostic applications where test reliability directly impacts treatment decisions . As precision medicine continues to evolve, DDB2 assessment using these advanced antibody reagents may become an important component of comprehensive tumor profiling and treatment planning.