PRKDC / DNA-dependent protein kinase catalytic subunit · IHC design guide

Design Immunohistochemistry for PRKDC

Plan PRKDC IHC in paraffin sections around the expected nuclear staining pattern (HPA tissue IHC). Use consistently fixed sections and assess nuclear signal; bone marrow hematopoietic cells provide a high-staining reference (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for PRKDC (IHC for PRKDC): expected localisation Predominantly nuclear in tissue sections (HPA tissue IHC), antibody M00645, validated IHC image, and IHC protocol steps
Printable PRKDC IHC protocol sheet — expected localisation Predominantly nuclear in tissue sections (HPA tissue IHC), antibody M00645, controls and protocol steps. Open the full PRKDC IHC guide →

PRKDC Immunohistochemistry Experimental Design Guide

Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.

Must know before staining
Expected localisation Predominantly nuclear in tissue sections (HPA tissue IHC)
Staining pattern Widespread nuclear staining across cell types (HPA tissue IHC)
Antigen retrieval Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen)
Positive control ⓘ Adipose tissue+4 more · see all
Negative control ⓘ None in HPA (detected in all 45 tissues); use no-primary + isotype controls
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M00645)
Caveat Broad staining limits tissue-negative controls (HPA tissue IHC)
Regulation Expression regulation is unreported (UniProt)
Isoform / epitope 2 isoforms; epitope coverage is unspecified (UniProt)
Section 1

Recommended PRKDC IHC & IF Protocols

Compare the catalog antibody's IHC-P protocol (datasheet) with 2 published PRKDC IHC methods (PMC13128572; PMC11084440).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human breast tissue; fixative not specified (datasheet M00645)
FixationImage fixative and duration unreported (datasheet M00645); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyRabbit monoclonal (clone EIA-16) anti-PRKDC, 1:50 (datasheet M00645)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultPRKDC-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control.
💡Decision noteStart with Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval rule: nuclear antigen); the ovarian study reports microwave retrieval without buffer or timing (PMC11084440).
Section 2

What Is the Expected PRKDC Staining Pattern?

PRKDC should show predominantly nuclear staining in paraffin sections: HPA describes a ubiquitous nuclear pattern with Supported IHC reliability and high staining in several listed cell populations (HPA tissue IHC). UniProt also places PRKDC in the nucleolus and cytosol and reports no transmembrane segment, so assess compartment and tissue context together (UniProt P78527).

What am I looking at on my slide?
Distinct nuclear chromogen in adipocytes, glandular cells, hematopoietic cells, respiratory epithelium, or the listed brain cells (HPA tissue IHC).This agrees with HPA's ubiquitous nuclear profile. Its listed high staining includes adipocytes, glandular cells, hematopoietic cells, respiratory epithelial cells, caudate glia, and cerebellar granular layer cells (HPA tissue IHC). Compare nuclei with the counterstain before scoring; HPA's Supported rating reflects agreement between antibody staining and RNA data, not a guarantee for every specimen (HPA tissue IHC).
Strong membrane or extracellular staining dominates while nuclei remain faint or clear (UniProt P78527 topology; HPA tissue IHC).Treat this as a suspect compartment pattern: PRKDC has no transmembrane segment, and HPA reports ubiquitous nuclear expression (UniProt P78527; HPA tissue IHC). UniProt also lists cytosol and nucleolus, so limited staining there alone does not establish an artefact (UniProt P78527). Check whether the suspect signal persists without primary antibody before interpreting it as PRKDC (general IHC practice).
Signal is restricted to an unexpected cell population while nuclei of adjacent HPA-listed cells lack staining (HPA tissue IHC).Check cell identity and tissue morphology first. HPA reports low tissue specificity and supplies no negative cell population, so staining outside its examples is not automatically cross-reactivity (HPA tissue IHC). If the signal is confined to a population with an implausible compartment pattern, investigate cross-reactivity or endogenous detection activity using appropriate controls (general IHC practice; HPA tissue IHC).
Brown deposit spreads across nuclei, cytoplasm, and empty areas, obscuring cell boundaries (general chromogenic IHC practice).This diffuse background prevents a reliable nuclear call against HPA's reported pattern (HPA tissue IHC). Inspect a no-primary control and assess blocking, washing, chromogen development, and antibody concentration as general IHC variables (general IHC practice). A background-free, compartment-resolved signal is needed before assigning cell-level PRKDC staining (general IHC practice).
No nuclear signal appears in a section containing an HPA-listed high-staining cell population (HPA tissue IHC).Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation.
💡Expected PRKDC appearanceCall a result consistent with PRKDC when predominant nuclear staining is clear in HPA-listed high-staining cells; treat dominant membrane, extracellular, or diffuse background signal as suspect (HPA tissue IHC; UniProt P78527 topology; general IHC practice).
How each factor affects the staining
Compartment: What should guide IHC scoring? (HPA tissue IHC; UniProt P78527)Prioritize discernible nuclear staining: HPA calls the tissue pattern ubiquitous and nuclear, while UniProt also lists nucleolus and cytosol (HPA tissue IHC; UniProt P78527). A cytosolic component therefore needs context; it should not replace the expected nuclear reference pattern (HPA tissue IHC; UniProt P78527).
Reference cells and validation (HPA tissue IHC; HPA antibodies)HPA lists High staining in eight supplied tissue and cell entries; it supplies no negative or low examples in this payload (HPA tissue IHC). Both listed antibodies have Supported IHC status, so use their observations as reference patterns while retaining antibody-specific controls (HPA antibodies; general IHC practice).
Isoforms and modifications (UniProt P78527)UniProt lists two isoforms and multiple modified residues, but this payload does not identify the catalog antibody's epitope or establish isoform-specific staining (UniProt P78527). Do not infer that a staining difference reflects an isoform or modification without epitope and validation evidence (UniProt P78527; general IHC practice).
IF/ICC Q&A: Where should the signal appear? (HPA subcellular ICC-IF)Expect enhanced nucleoplasmic localization in HPA's ICC-IF record; its image list includes A-431, Hep-G2, and U2OS, and antibody HPA035174 has Enhanced ICC status (HPA subcellular ICC-IF; HPA antibodies). That cell imaging evidence supports an IF localization check, not an IHC-P protocol choice (HPA subcellular ICC-IF; HPA antibodies).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Nuclei are blank in a tissue containing HPA-listed high-staining cells (HPA tissue IHC).The expected cells may be absent from the evaluated field, or the staining run may have failed; the slide alone cannot distinguish these possibilities (HPA tissue IHC; general IHC practice).Locate the listed cells morphologically, check a positive control, then review the catalog antibody's IHC-P retrieval, dilution, and detection instructions (HPA tissue IHC; general IHC practice).
Most signal lies at cell borders or outside cells (HPA tissue IHC; UniProt P78527 topology).That distribution conflicts with HPA's nuclear pattern and UniProt's lack of a transmembrane segment; nonspecific deposition or detection background is possible (HPA tissue IHC; UniProt P78527; general IHC practice).Compare a no-primary control, inspect the counterstained nuclei, and score PRKDC only where compartment-resolved signal supports the nuclear pattern (HPA tissue IHC; general IHC practice).
All compartments appear uniformly dark, obscuring nuclei (general chromogenic IHC practice).Excess antibody, inadequate washing, or overdevelopment can produce diffuse chromogenic background in IHC generally; this record does not assign a PRKDC-specific cause (general IHC practice).Check the no-primary control, then adjust dilution, washing, or development according to the catalog IHC-P method while retaining a positive control (general IHC practice).
A suspicious cell population stains, but expected nearby nuclei do not (HPA tissue IHC).HPA's low tissue specificity and absence of listed negative cells limit any exclusion by cell identity alone; cross-reactivity or endogenous detection activity remains possible (HPA tissue IHC; general IHC practice).Confirm morphology, run no-primary and detection-system controls as appropriate, and compare the suspect signal with the reported nuclear pattern (HPA tissue IHC; general IHC practice).
Cytoplasmic signal accompanies a weaker nuclear signal (UniProt P78527; HPA tissue IHC).UniProt lists cytosol as a PRKDC location, while HPA's tissue IHC profile emphasizes nuclei; this combination alone cannot establish a failed assay (UniProt P78527; HPA tissue IHC).Score nuclear and cytoplasmic compartments separately, inspect controls for background, and report the observed distribution without assigning an unsupported cause (UniProt P78527; HPA tissue IHC; general IHC practice).

Sample controls for PRKDC IHC & IF

🧪Run breast first and look for staining in glandular cells (HPA: High in breast glandular cells; M00645 tissue-IHC caption: human breast). HPA detects PRKDC in all 45 scored tissues, so there is no HPA-supported negative tissue; use no-primary and isotype controls, and expect cells without specific signal on the positive slide to show only background staining (HPA: no negative rows; standard IHC practice).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: PRKDC is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PRKDC in A-431, Hep-G2, U2OS, U2OS, siRNA 1 (10x), U2OS, siRNA 1 (40x), U2OS, siRNA 2 (10x), U2OS, siRNA 2 (40x), U2OS, scrambled (10x), U2OS, scrambled (40x), with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; an isotype control matched to the primary antibody’s host species and immunoglobulin class, with comparable antibody format; and a PRKDC knockout biological negative where available (standard IHC practice). For chromogenic breast IHC, block endogenous peroxidase and check blood-rich areas for background staining (standard IHC practice).
⚠️Feasibility: The supplied evidence reports no PRKDC-specific fixation window or fixation effect, and the M00645 paraffin-section breast caption does not state a fixative (M00645 tissue-IHC caption). Retrieval dependence is unreported, so optimize antigen retrieval for the paraffin sections; the evidence does not establish whether frozen sections or IF/ICC would be easier (standard IHC practice; M00645 tissue-IHC caption). Assess nuclear staining against the controls, while accounting for possible peroxidase background in blood-rich areas of breast sections (HPA subcellular: nucleoplasm; standard IHC practice).

HPA tissue IHC evidence for PRKDC

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes High Protein (IHC) HPA →
Adrenal gland Glandular cells High Protein (IHC) HPA →
Appendix Glandular cells High Protein (IHC) HPA →
Bone marrow Hematopoietic cells High Protein (IHC) HPA →
Breast Glandular cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: PRKDC is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced PRKDC IHC Tips

Troubleshoot PRKDC staining by checking nuclear signal against retrieval, specimen handling, antibody specificity, and tissue controls.

What retrieval should I try first when PRKDC nuclear staining is weak?
For paraffin-section PRKDC IHC, use Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval rule: nuclear antigen). Compare a known positive section in the same run, such as breast glandular cells, where high staining is reported, and judge whether nuclei gain signal without diffuse tissue staining (HPA: High in breast glandular cells; standard IHC practice). If signal remains weak, verify that the primary antibody is validated for IHC on paraffin sections and that detection reagents work on a separate control (catalog caption: paraffin-embedded human breast; standard IHC practice). Record the retrieval conditions with each run so that differences in heating or cooling can be distinguished from specimen variation (standard IHC practice).
Could fixation explain inconsistent PRKDC staining between paraffin sections?
Target-specific sensitivity of PRKDC staining to fixation is unknown from the supplied evidence; the catalog caption identifies paraffin-embedded human breast but does not state its fixative (catalog caption: M00645). Document each specimen’s fixative, fixation duration, processing history, and section age before comparing nuclear intensity, because these variables can affect IHC staining generally (standard IHC practice). Run sections from differently handled specimens together with the same Tris-EDTA pH 9.0 retrieval and 20 min heating step to limit run variation (page retrieval rule; standard IHC practice). If one batch remains weak, assess morphology and staining controls before assigning the difference to PRKDC abundance (standard IHC practice).
Should cytoplasmic or nucleolar PRKDC staining count as specific?
Score nucleoplasmic staining as the primary expected pattern, since the tissue profile reports ubiquitous nuclear expression and subcellular imaging places PRKDC in the nucleoplasm (HPA: tissue IHC and subcellular profile). Nuclear and nucleolar locations, as well as cytosolic localisation, are also annotated, so a minor non-nucleoplasmic signal is not automatically artefactual (UniProt P78527: subcellular location). PRKDC has no transmembrane segment, making a crisp membrane-only pattern a reason to investigate staining specificity (UniProt P78527: topology; standard IHC practice). Compare compartments within intact cells on the same section, using the counterstain to define nuclei and excluding folds or damaged areas from localisation calls (standard IHC practice).
How can epitope choice change the PRKDC IHC result?
Check the antibody’s immunogen or mapped epitope against both annotated PRKDC isoforms before interpreting a negative section, because the record lists 2 isoforms without defining this antibody’s epitope (UniProt P78527: isoforms; supplied catalog caption). PRKDC is a 4128-residue protein with FAT, catalytic, and FATC regions, so an epitope location can matter when comparing antibodies (UniProt P78527: sequence and domains; standard IHC practice). The record also lists phosphorylation and acetylation sites; their presence alone does not establish that they alter this antibody’s staining (UniProt P78527: modified residues). For discordant results, compare independently validated epitopes on adjacent sections and keep retrieval and detection conditions matched (standard IHC practice).
How should I design a companion PRKDC multiplex IF experiment?
For a companion IF experiment, pair PRKDC with a marker identifying the expected cell population and a nuclear counterstain, then assess PRKDC within those marked cells (standard IF practice). Choose spectrally separated fluorophores and place the weaker expected signal in a channel with low tissue autofluorescence, checking an unstained section before interpreting multiplex overlap (standard IF practice). Permeabilise sufficiently for antibody access to the intracellular epitope; PRKDC has no transmembrane segment and its main reported IF location is nucleoplasmic (UniProt P78527: topology; HPA: subcellular profile; standard IF practice). HPA includes ICC/IF images, but they do not establish IF performance for catalog antibody M00645 (HPA: subcellular profile; catalog caption: M00645).
How can I distinguish PRKDC signal from chromogenic IHC background?
Assess a no-primary control beside the stained section to reveal detection-reagent background, and include a peroxidase-block step when using an enzyme-based chromogenic workflow (standard IHC practice). Titrate the IHC-validated antibody according to its documented instructions rather than assuming that stronger brown signal improves specificity; the supplied caption provides no working dilution (catalog caption: M00645; standard IHC practice). Inspect tissue edges, folds, pigment, and necrotic regions separately, since local deposits can imitate cellular staining (standard IHC practice). A credible PRKDC result should include interpretable nuclear staining in intact cells, consistent with the reported tissue and subcellular patterns (HPA: ubiquitous nuclear expression and nucleoplasmic localisation).
What should I score when comparing PRKDC across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the analysed cell population and score nuclear PRKDC with the percentage of positive cells or an H-score, recording intensity categories consistently across slides (standard IHC practice; HPA: ubiquitous nuclear expression). Normalise each result to the number of evaluable nuclei in the same annotated tissue compartment, and report excluded necrotic or folded areas (standard IHC practice). If spatial abundance matters, report positive nuclei per mm² alongside the percentage so that cell density and staining frequency remain distinguishable (standard IHC practice). Use the same retrieval and detection settings across the comparison, and treat cytoplasmic signal as a separately recorded observation (page retrieval rule; UniProt P78527: cytosolic location; standard IHC practice).
When is a PRKDC-positive IHC result biologically credible?
Expect staining in intact nuclei across many tissue cell types, with high staining reported in breast glandular cells and several other listed populations (HPA: ubiquitous nuclear expression; HPA: positive tissue entries). A membrane-only pattern conflicts with PRKDC’s lack of a transmembrane segment, while cytosolic or nucleolar staining needs separate assessment because those locations are annotated (UniProt P78527: topology and subcellular location). Discount signal limited to section edges, necrotic zones, or no-primary controls, and investigate residual endogenous enzyme activity in chromogenic detection (standard IHC practice). Finally, interpret staining as protein localisation or abundance, not direct evidence of kinase activity or DNA repair, which require separate measurements (UniProt P78527: function; standard IHC practice).
Boster reagents

Best PRKDC / DNA-dependent protein kinase catalytic subunit IHC Antibodies

Three anti-PRKDC antibodies have IHC images from paraffin-embedded human breast, colon, and brain (IHC captions); all three list IF, with species coverage specified in the catalog (catalog applications/reactivity).

Real IHC data Immunohistochemical analysis of paraffin-embedded human breast, using DNA-PKcs Antibody.
Anti-DNA-PKcs PRKDC Rabbit Monoclonal Antibody
Cat # M00645
Real IHC data Immunohistochemical analysis of paraffin-embedded human colon tissue using anti-Phospho-DNA PKcs (S2056) antibody. The section was pre-treated using heat mediated antigen retrieval with Tris-EDTA buffer (pH 9.0) for 20 minutes.The tissues were blocked in 5% BSA for 30 minutes at room temperature, washed with ddH2O and PBS, and then probed with the primary antibody (1/200) for 30 minutes at room temperature. The detection was performed using an HRP conjugated compact polymer system. DAB was used as the chromogen. Tissues were counterstained with hematoxylin and mounted with DPX.
Anti-Phospho-DNA PKcs (S2056) PRKDC Rabbit Monoclonal Antibody
Cat # P00645
Real IHC data Immunohistochemical analysis of paraffin-embedded Human brain. Antibody was diluted at 1:100 (4° overnight). High-pressure and temperature Tris-EDTA, pH8.0 was used for antigen retrieval. Negetive contrl (right) obtaned from antibody was pre-absorbed by immunogen peptide.
Anti-Phospho-DNA-PKCS (S2612) PRKDC Antibody
Cat # A00645S2612

M00645 has a human breast IHC image and lists IF/ICC for human, mouse, and rat; P00645 has human colon and colon carcinoma IHC images and lists IF/ICC for human (IHC captions; catalog applications/reactivity). A00645S2612 has a human brain IHC image and lists IF for human, mouse, and rat (IHC caption; catalog applications/reactivity).

Which to pick: For paraffin-section IHC, choose M00645 to detect total PRKDC in human breast (M00645 title and IHC caption), P00645 to detect phospho-S2056 in human colon (P00645 title and IHC caption), or A00645S2612 to detect phospho-S2612 in human brain (A00645S2612 title and IHC caption). For IF/ICC and human, mouse, or rat samples, M00645 is the rabbit monoclonal with both applications listed; A00645S2612 lists IF and the same species, while P00645 lists IF/ICC for human only (catalog applications/reactivity/host/clone). The P00645 colon caption reports Tris-EDTA pH 9.0 retrieval for 20 minutes and primary antibody at 1:200, whereas its catalog IHC dilution is 1:50; the A00645S2612 brain caption reports Tris-EDTA pH 8.0 retrieval and 1:100 primary antibody, and fixative is unreported in all three captions (IHC captions; catalog IHC dilutions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry P78527 (PRKDC_HUMAN, DNA-dependent protein kinase catalytic subunit).
  2. Human Protein Atlas. PRKDC tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. PRKDC subcellular location (ICC-IF): Localized to the nucleoplasm..
  4. Human Protein Atlas. PRKDC antibody validation summary (2 antibodies).
  5. High expression of PRKDC promotes breast cancer cell growth via p38 MAPK signaling and is associated with poor survival. Molecular genetics & genomic medicine 2019 — PMC6825841.
  6. Ribosome biogenesis programs define a three-gene RBscore with prognostic relevance in bladder cancer. Frontiers in immunology 2026 — PMC13128572.
  7. PRKDC-Mediated NHEJ May Play a Crucial Role in Aneuploidy of Chromosome 8-Driven Progression of Ovarian Cancer. International journal of molecular sciences 2024 — PMC11084440.
  8. Unconventional activation of PRKDC by TNF-α: deciphering its crucial role in Th1-mediated inflammation beyond DNA repair as part of the DNA-PK complex. Journal of inflammation (London, England) 2024 — PMC11059672.
  9. PubMed PMID:7671312 — UniProt-cited evidence.
  10. PubMed PMID:11418067 — UniProt-cited evidence.
  11. PubMed PMID:9284934 — UniProt-cited evidence.