DDB2 Recombinant Monoclonal Antibody

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Description

DDB2 Function and Pathophysiology

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).

Antibody Characteristics

Recombinant monoclonal antibodies (rMAbs) are produced via engineered expression systems, offering advantages over traditional methods:

FeatureRecombinant rMAbsTraditional MAbs
ProductionDefined genetic sequences, batch consistencyHybridoma-dependent, variable
SpecificityEngineered binding regions for affinityLimited epitope targeting
Cross-reactivityControlled via sequence designHigher risk of off-target binding
ApplicationsTherapeutic/diagnostic engineeringPrimarily research use

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Detection and Validation Techniques

DDB2 rMAbs are validated for:

ApplicationDilution RangeKey Findings
Western Blot1:500–1:2000Detects 48–51 kDa bands in HeLa, A431, and mouse kidney/liver lysates (3, 9, 11)
Immunofluorescence1:50–1:200Localizes DDB2 to nuclear regions, colocalizing with UV-induced DNA damage (3, 11)
ELISAVariesQuantifies DDB2 levels in cell lysates or tissue extracts (5, 9)
ImmunoprecipitationN/AIdentifies DDB2 interactions with CUL4A and ROC1 (4, 8)

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DNA Repair Dynamics

  • 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).

Interactions and Pathways

  • 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).

Quality Control and Validation

Validation MethodCriteriaExample
Western BlotSpecific 48–51 kDa band in positive controlsHeLa lysates show strong signal at 1:2000
ImmunofluorescenceNuclear localization post-UV treatmentDAPI/UV damage colocalization in MCF7 cells
Cross-reactivityNo off-target binding to non-human proteinsNo signal in rabbit secondary antibody tests

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Product Specs

Buffer
Rabbit IgG in phosphate buffered saline, pH 7.4, 150mM NaCl, 0.02% sodium azide and 50% glycerol.
Description

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.

Form
Liquid
Lead Time
Typically, we can dispatch products within 1-3 working days after receiving your order. Delivery times may vary depending on the purchase method and location. Please consult your local distributors for specific delivery timelines.
Synonyms
DNA damage-binding protein 2 (DDB p48 subunit) (DDBb) (Damage-specific DNA-binding protein 2) (UV-damaged DNA-binding protein 2) (UV-DDB 2), DDB2
Target Names
Uniprot No.

Target Background

Function

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.

Gene References Into Functions
  1. A study identified a novel mutation DDB2 p. (Lys381Argfs*2) present in a homozygous state in 5 affected individuals from the same Tunisian family with Xeroderma pigmentosum. PMID: 29169765
  2. Chronic low-dose UVB (CLUV) treatment activates p53, correlating with increased levels of DDB2 and XPC proteins. DDB2 and XPC are recruited to chromatin-bound sites, suggesting more efficient cyclobutane pyrimidine dimer (CPD) recognition by NER and more effective CPD repair. PMID: 29448173
  3. DDB2-PCNA interaction might contribute to a proper DNA damage response for maintaining genome integrity. PMID: 29604309
  4. DDB2 undergoes SUMOylation upon ultraviolet irradiation, and this post-translational modification plays a crucial role in the initial recognition and processing of UV-induced DNA damage within chromatin. PMID: 28981631
  5. Research indicates that DDB2 is essential for chromatin association of XRCC5/6 in the absence of DNA damage and provides evidence that XRCC5/6 are functional partners of DDB2 in its transcriptional stimulatory activity. PMID: 28035050
  6. UVRAG acts as a regulator of CRL4(DDB2)-mediated nucleotide excision repair, and its expression levels may influence melanoma predisposition. PMID: 27203177
  7. High DDB2 expression is associated with increased radioresistance in non-small cell lung cancer. PMID: 27553023
  8. Data suggests that DDB2 is involved in early events during metastatic progression of breast cancer cells and may serve as a marker for metastatic progression in this type of cancer. PMID: 26879405
  9. DDB2 polymorphisms are linked to risks of gastric cancer and atrophic gastritis. PMID: 26760766
  10. The release of NER components like DNA damage binding protein 2 (DDB2) and Xeroderma Pigmentosum complementation group C protein (XPC) following oxidative stress might potentially involve their apoptotic role rather than their DNA repair function. PMID: 26263968
  11. PKM2 interacts with DDB2 and reduces cell survival upon UV irradiation. PMID: 26410533
  12. DDB2 can bind to the promoter region of NEDD4L and recruit enhancer of zeste homolog 2 histone methyltransferase to repress NEDD4L transcription by enhancing histone H3 lysine 27 trimethylation at the NEDD4L promoter. PMID: 26130719
  13. Data demonstrated that the DDB2 IRES activity was promoted during stress conditions. These findings reveal a novel mechanism contributing to DDB2 expression. PMID: 26187069
  14. DDB2 is involved in the ubiquitination and degradation of PAQR3 in gastric cancer cells. PMID: 26205499
  15. DDB2 rs747650 is implicated in androgen metabolism, inflammatory processes, and scar formation in severe acne. PMID: 24399259
  16. DDB2 plays a crucial role in DNA damage-induced ROS accumulation, ROS-induced premature senescence, and inhibition of skin tumorigenesis. PMID: 23109835
  17. DDB2 is protected from ubiquitination and degradation by XPC in a stochastic manner. This allows XPC to enable DDB2 to initiate multiple rounds of repair events, contributing to the persistence of cellular DNA repair capacity. PMID: 25628365
  18. DDB2 protein expression is low in ovarian tumor cells. PMID: 24574518
  19. Chromatin retention of DNA damage sensors DDB2 and XPC due to loss of p97 segregase causes genotoxicity. PMID: 24770583
  20. DDB2 is a PCNA-binding protein, and this association is required for DDB2 proteolytic degradation. PMID: 24200966
  21. A study provides new insights into the posttranslational regulation of DDB2 and expands the biological functions of protein alpha-N-methylation to DNA repair. PMID: 24753253
  22. Data indicate that p53-dependent upregulation of XPC and DDB2 is a key mechanism upon genotoxic stress, whereby melanoma cells acquire resistance towards DNA cross-linking agents. PMID: 23604128
  23. DDB2 and a DDB2-ATM feedback loop influence HCMV replication. PMID: 24335308
  24. Knockdown of DDB2-induced IkappaBalpha gene expression restored NF-kappaB activity. PMID: 23774208
  25. These findings suggest that the SUMOylation of DDB2 facilitates CPD repair. PMID: 23860269
  26. DDB2 facilitates ATR and ATM recruitment to the DNA damage site following UV irradiation. PMID: 23422745
  27. Results indicate a transcriptional regulatory pathway of DDB2 that is directly linked to the mechanisms that suppress metastasis of colon cancer. PMID: 23610444
  28. The 3'untranslated region of DDB2 contains a cis-acting element that affects stability, export, and translation of the message. PMID: 23605047
  29. Data suggest that poly(ADP-ribose) polymerase-1 (PARP-1) collaborates with DNA-binding protein 2 (DDB2) to increase the efficiency of the lesion recognition step of the global genomic subpathway of NER (GG-NER). PMID: 23319653
  30. DDB2 can inhibit cell growth rate in AR-expressing cells (LNCaP) but not in AR-null cells (PC3). PMID: 22846800
  31. Data supports a model where poly(ADP-ribosyl)ation of DDB2 suppresses DDB2 ubiquitylation and outlines a molecular mechanism for PARP1-mediated regulation of nucleotide excision repair through DDB2 stabilization and recruitment of the chromatin remodeler ALC1. PMID: 23045548
  32. A study reports a new function of DDB2 in modulating chromatin structure at DNA lesions. PMID: 22492724
  33. The DDB2 subunit of UV-DDB associates transiently with the DNA-binding domain of XPC to fine-tune its engagement with CPD lesions. PMID: 22039351
  34. Nucleotide excision repair proteins rapidly accumulate but fail to persist in human xeroderma pigmentosum XP-E (DDB2 mutant) cells. PMID: 21388382
  35. Multiple skin cancers in adults are associated with mutations in the XP-E (DDB2) DNA repair gene. PMID: 21107348
  36. Overexpression of DDB2 enhances the sensitivity of ovarian cancer cells to cisplatin by augmenting cellular apoptosis. PMID: 20013802
  37. Damaged DNA-binding protein 2 (DDB2) protects against UV irradiation in human cells and Drosophila. PMID: 20398405
  38. Data shows that XPC and Ku oppositely regulate the ubiquitin ligase activity of DDB2, and that DDB2 complex-mediated ubiquitylation plays a role in recruiting XPA to damaged sites. PMID: 20368362
  39. These results indicate that DDB2 is a modulator of UV-induced apoptosis, and that UV resistance can be overcome by inhibition of DDB2. PMID: 11852074
  40. These findings demonstrate direct activation of the human DDB2 gene by p53. The corresponding region in the mouse DDB2 gene shared significant sequence identity with the human gene but was deficient for p53 binding and transcriptional activation. PMID: 11971958
  41. BRCA1 upregulates DDB2, with some evidence suggesting that p53 is involved in its regulation. PMID: 12496474
  42. Overexpression of DDB2 in V79 cells potentiates DNA repair and protects cells from UV-induced apoptosis and cytotoxicity. PMID: 12553360
  43. DDB2p48 and CSA are each integrated into nearly identical complexes via interaction with DDB1. PMID: 12732143
  44. DDB2p48 activates the recruitment of XPC to cyclobutane pyrimidine dimers and may be the initial recognition factor in the nucleotide excision repair pathway. PMID: 12944386
  45. Data suggests that both before and after UV irradiation, DDB2 directly regulates p53 levels, while DDB2 expression is itself regulated by p53. PMID: 14560002
  46. Identification of four DDB2 variants from HeLa cells (D1-D4) that are generated by alternative splicing. PMID: 14751237
  47. DDB2 regulates TNF signaling-mediated apoptosis via cFLIP and contributes to acquired cross-resistance. PMID: 15644494
  48. UV-DDB interacts physically with XPC, and both are polyubiquitylated by the UV-DDB-ubiquitin ligase complex. PMID: 15882621
  49. DDB2 possesses intrinsic damaged DNA binding activity. PMID: 16260596
  50. CUL-4A mediates the proteolytic degradation of DDB2, and this degradation event, initiated at the lesion sites, regulates damage recognition by XPC. PMID: 16527807

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Database Links

HGNC: 2718

OMIM: 278740

KEGG: hsa:1643

STRING: 9606.ENSP00000256996

UniGene: Hs.700338

Involvement In Disease
Xeroderma pigmentosum complementation group E (XP-E)
Protein Families
WD repeat DDB2/WDR76 family
Subcellular Location
Nucleus. Note=Accumulates at sites of DNA damage following UV irradiation.
Tissue Specificity
Ubiquitously expressed; with highest levels in corneal endothelium and lowest levels in brain. Isoform D1 is highly expressed in brain and heart. Isoform D2, isoform D3 and isoform D4 are weakly expressed.

Q&A

What is DDB2 and why is it important in research?

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.

What applications are DDB2 recombinant monoclonal antibodies validated for?

DDB2 recombinant monoclonal antibodies have been validated for multiple research applications:

ApplicationCommon DilutionsNotes
Western Blotting (WB)1:500-1:16000Typically detects bands at 47-51 kDa
Immunohistochemistry (IHC)1:50-1:200Effective for paraffin-embedded tissues
Flow Cytometry (FC)1:50-1:200For cell surface and intracellular detection
Immunocytochemistry (ICC)1:50-1:200For cellular localization studies
Immunofluorescence (IF)1:50-1:200For subcellular localization visualization
ELISAVaries by manufacturerFor quantitative detection

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 .

How should DDB2 recombinant monoclonal antibodies be stored to maintain optimal activity?

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

  • pH maintained at approximately 7.3-7.4

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

  • Mix gently to ensure homogeneity before pipetting

Following these storage guidelines will ensure consistent results and extend the usable life of the antibody preparation.

How can I validate the specificity of a DDB2 recombinant monoclonal antibody for my experimental system?

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.

What are the critical factors for optimizing Western blot protocols using DDB2 recombinant monoclonal antibodies?

Western blot optimization for DDB2 detection requires attention to several critical factors:

  • Sample preparation:

    • Use appropriate lysis buffers containing protease inhibitors to prevent DDB2 degradation

    • Nuclear extraction protocols may improve detection as DDB2 is predominantly nuclear

    • Determine optimal protein loading (typically 20-40 μg of total protein)

  • 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:

    • Primary antibody: Start with manufacturer's recommendation (typically 1:500-1:2000) and optimize

    • Secondary antibody: Usually 1:5000-1:50000 depending on detection system sensitivity

  • 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:

    • Look for a distinct band at 47-51 kDa

    • Some antibodies may detect multiple bands if alternative splice variants or post-translational modifications are present

Detailed optimization records should be maintained to ensure reproducibility across experiments.

What considerations are important when using DDB2 recombinant monoclonal antibodies for immunohistochemistry?

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:

    • Heat-induced epitope retrieval (HIER) in citrate buffer (pH 6.0) under high pressure has been successful for DDB2 detection

    • Optimize time and temperature for your specific tissue type

  • Blocking parameters:

    • 10% normal goat serum for 30 minutes at room temperature has been effective

    • Match blocking serum to the species of secondary antibody

  • Antibody dilution and incubation:

    • Start with dilutions of 1:50-1:200 as recommended by manufacturers

    • Incubate primary antibody at 4°C overnight for optimal results

  • Detection systems:

    • Polymer-based detection systems (e.g., goat anti-rabbit polymer IgG labeled by HRP) provide high sensitivity and low background

    • DAB (3,3'-diaminobenzidine) concentration at approximately 0.46% yields good visualization

  • Controls and interpretation:

    • Include positive control tissues (e.g., salivary gland, cervical cancer tissues)

    • DDB2 staining should be primarily nuclear with possible cytoplasmic localization

    • Quantify staining using appropriate scoring systems (H-score, percentage positive cells, or intensity scales)

  • 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.

How do recombinant monoclonal antibodies for DDB2 differ from traditional monoclonal and polyclonal antibodies in research applications?

Recombinant monoclonal antibodies represent a significant advancement over traditional antibody technologies, with several key advantages for DDB2 research:

CharacteristicRecombinant MonoclonalTraditional MonoclonalPolyclonal
Production methodIn vitro expression from cloned DNA sequences Hybridoma technologyAnimal immunization
Batch consistencyExcellent Good but diminishes over timeVariable
SpecificityVery high, consistent HighVariable, recognizes multiple epitopes
SensitivityEnhanced GoodOften high but variable
ReproducibilityExcellent Diminishes as hybridomas ageLow
Supply sustainabilityUnlimited Limited by hybridoma lifespanLimited by animal serum
Production ethicsAnimal-free options available Requires animal immunizationRequires animal immunization
Application in complex assaysExcellent due to consistencyGoodLimited by specificity concerns
CostInitially higher but consistentVariableGenerally lower

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 .

What approaches can resolve conflicting results when using different DDB2 antibodies in the same experimental system?

Resolving conflicting results with different DDB2 antibodies requires systematic troubleshooting and validation:

  • Epitope mapping comparison:

    • Different antibodies target distinct regions of DDB2

    • Compare the epitopes recognized by each antibody (e.g., one targets amino acids surrounding Ala174 , another might target a different region)

    • Structural accessibility of epitopes may differ in various experimental conditions

  • 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.

How can DDB2 recombinant monoclonal antibodies be used to investigate the role of DDB2 in cancer pathways?

DDB2 recombinant monoclonal antibodies provide powerful tools for investigating DDB2's role in cancer pathways through multiple experimental approaches:

  • Expression profiling across cancer types:

    • Use validated antibodies in tissue microarrays to quantify DDB2 expression across cancer stages and types

    • Correlate expression with clinical outcomes and molecular subtypes

    • DDB2 has shown particular relevance in breast cancer, where it may function as an oncogene and potential predictive marker

  • 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:

    • Perform ChIP-seq using DDB2 antibodies to identify genomic binding sites

    • Integrate with RNA-seq data to correlate binding with transcriptional changes

    • Investigate DDB2's reported negative regulation of SOD2 gene expression in breast cancer cells

  • 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.

What are the most common causes of false positive or false negative results when using DDB2 recombinant monoclonal antibodies, and how can they be addressed?

Understanding and mitigating false results is essential for reliable DDB2 research:

False Positive Causes and Solutions:

  • Cross-reactivity with related proteins:

    • Issue: WD-repeat family proteins share structural similarities

    • Solution: Validate specificity using knockout controls and peptide competition assays

    • Implementation: Pre-incubate antibody with immunizing peptide to block specific binding

  • 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:

    • Issue: Formalin cross-linking can hide antibody binding sites

    • Solution: Optimize antigen retrieval methods

    • Implementation: Test multiple retrieval methods, including high-pressure citrate buffer (pH 6.0)

  • 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:

    • Issue: Modifications may alter epitope recognition

    • Solution: Use multiple antibodies recognizing different epitopes

    • Implementation: Compare antibodies targeting different regions of DDB2

  • 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:

    • Issue: Repeated freeze-thaw cycles reduce activity

    • Solution: Aliquot antibodies upon receipt and store properly

    • Implementation: Store at recommended temperatures (-20°C or -80°C) and avoid repeated freezing

Systematic controls and thorough validation are essential for distinguishing true results from artifacts.

How should researchers approach comparison of DDB2 expression across different tissue types or experimental conditions?

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:

    • Include common reference samples across all experiments

    • Use recombinant DDB2 protein standards for absolute quantification

    • When possible, include samples with known DDB2 expression levels (e.g., PC-3, HeLa cells)

  • 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.

What methodological considerations are important when using DDB2 recombinant monoclonal antibodies in flow cytometry for cell cycle or DNA damage studies?

Flow cytometry applications with DDB2 recombinant monoclonal antibodies require specific methodological considerations:

  • Cell preparation optimization:

    • Fixation method: 4% formaldehyde provides good epitope preservation

    • Permeabilization: Optimize buffer type (Triton X-100, saponin, methanol) and concentration

    • Single-cell suspension: Ensure complete dissociation and minimal clumping

    • Strain cells through 40-70 μm mesh to remove aggregates

  • 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:

    • Titrate antibody in range of 1:50-1:200 to optimize signal-to-noise ratio

    • Include isotype controls matched to antibody concentration

    • Use positive controls (e.g., A549 cells) and negative controls (knockdown cells)

    • Include fluorescence-minus-one (FMO) controls for multicolor panels

  • 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.

How can DDB2 recombinant monoclonal antibodies be integrated into high-throughput screening approaches for DNA damage response modulators?

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.

What are the challenges and potential solutions when developing site-specific phosphorylation antibodies for DDB2?

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 MethodExpected ResultInterpretation
Lambda phosphatase treatmentSignal eliminationConfirms phospho-specificity
Phospho-null mutation (S→A)Signal eliminationConfirms site-specificity
Phospho-mimetic (S→E)No detectionConfirms true phospho-recognition
UV damage time courseSignal increaseConfirms biological relevance
ATR/ATM inhibitor pretreatmentSignal reductionValidates pathway involvement
Competition with phos-peptideSignal eliminationConfirms epitope specificity
Competition with non-phos peptideNo effectConfirms 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.

How might DDB2 recombinant monoclonal antibodies contribute to precision medicine approaches in cancer treatment?

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.

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