The FAR1 antibody, FITC conjugated is a fluorescently labeled primary antibody designed to detect Fatty acyl-CoA reductase 1 (FAR1), an enzyme critical for fatty alcohol biosynthesis and ether lipid production. FITC (fluorescein isothiocyanate) is covalently attached to the antibody’s lysine residues, enabling visualization via fluorescence microscopy. This conjugate facilitates applications in immunofluorescence (IF), immunohistochemistry (IHC), and Western blotting (WB) to study FAR1 localization, expression, and functional roles .
FITC-conjugated FAR1 antibodies are used to localize FAR1 to peroxisomes, as demonstrated in human cell lines (e.g., RT-4) . Optimal dilutions range from 0.25–2 μg/mL . For paraffin-embedded sections, dilutions of 1:50–200 are recommended .
HPA017322 (Sigma-Aldrich): Detects FAR1 in cytoplasmic regions of human kidney tubules at 1:20–1:50 dilution .
NBP1-89847 (Bio-Techne): Requires antigen retrieval (e.g., HIER pH 6) for paraffin sections .
FAR1 antibodies are validated for WB at 0.04–0.4 μg/mL . For example, HPA017322 detects FAR1 in human cardiac myocytes under ER stress .
Binding Affinity: Higher FITC labeling indices correlate with reduced antigen-binding affinity, necessitating careful optimization .
Non-Specific Staining: FITC-conjugated antibodies may exhibit increased background noise, requiring blocking agents (e.g., fetal bovine serum) .
Stability: FITC is light-sensitive; antibodies should be stored in the dark at −20°C .
| Application | Dilution | Fixation | Imaging |
|---|---|---|---|
| IF (Cell Lines) | 0.25–2 μg/mL | PFA/Triton X-100 | FITC filter |
| IHC (Paraffin) | 1:20–1:50 | HIER retrieval | Fluorescence microscopy |
| WB | 0.04–0.4 μg/mL | N/A | Chemiluminescence |
Neurological Disorders: De novo FAR1 variants (e.g., R480C) disrupt plasmalogen feedback regulation, leading to spastic paraparesis and congenital cataracts. Antibodies like HPA017322 confirmed elevated FAR1 protein levels in patient fibroblasts .
Ether Lipid Synthesis: Biallelic FAR1 mutations cause plasmalogen deficiency, while dominant variants increase ether lipid production .
Peroxisomal Localization: FAR1 colocalizes with peroxisomal markers in cardiac myocytes, implicated in ER stress responses .
Hepatic Clearance: FITC-conjugated peptides are rapidly cleared by liver sinusoidal endothelial cells (LSECs) and hepatocytes, suggesting caution in in vivo imaging .
FAR1 (fatty acyl CoA reductase 1) is a protein with a calculated molecular weight of 59 kDa, comprising 515 amino acids. It functions primarily in fatty acid metabolism, catalyzing the reduction of fatty acyl-CoAs to fatty alcohols. FAR1 has been studied across multiple species including humans, mice, and rats. For research purposes, it's important to note that human FAR1 is encoded by gene ID 84188 with GenBank accession number BC017377 .
When designing experiments involving FAR1 antibodies, consider that this protein may demonstrate tissue-specific expression patterns and could be involved in multiple metabolic pathways, requiring careful experimental control selection.
FITC (Fluorescein Isothiocyanate) conjugation occurs through the formation of a covalent bond between the isothiocyanate group of the fluorescein molecule and primary/secondary amine groups on the antibody, typically at lysine residues. The reaction is highly pH-dependent, with optimal conjugation occurring at alkaline pH (approximately 9.5) where amine groups are sufficiently deprotonated .
The conjugation process follows this reaction mechanism:
Protein-NH₂ + FITC → Protein-NH-CS-FITC
This thiourea linkage is stable and allows for fluorescent detection of the antibody
Maximal labeling is achieved under specific conditions:
Reaction temperature: 25°C (room temperature)
pH: 9.5
Initial protein concentration: 25 mg/ml
For maintaining optimal activity and fluorescence of FITC-conjugated FAR1 antibodies:
Storage temperature: -20°C is recommended
Buffer composition: PBS with 0.02% sodium azide and 50% glycerol at pH 7.3
Stability period: Typically stable for one year after shipment under proper storage conditions
Light protection: Critical to prevent photobleaching as continuous light exposure causes gradual fluorescence loss
Aliquoting: May be unnecessary for -20°C storage for some preparations, but helps avoid repeated freeze-thaw cycles
FITC-conjugated antibodies, including those targeting FAR1, are extensively utilized in:
Immunofluorescence detection on fixed cells and tissues
Flow cytometry for quantitative analysis of protein expression
Fluorescence microscopy for localization studies
Tissue cross-reactivity (TCR) studies for therapeutic antibody development
Protein-protein interaction analyses
Cellular uptake and trafficking investigations
Transport and permeability studies across cell monolayers
Microsequencing applications
The direct fluorescent labeling eliminates the need for secondary antibody incubation steps, reducing experimental complexity and potential sources of background.
Determining optimal antibody dilution requires systematic titration:
Starting point: For immunofluorescence on mammalian cells, begin with 1:500 dilution in PBS containing 10% fetal bovine serum (FBS)
Titration approach: Test serial dilutions (e.g., 1:250, 1:500, 1:1000)
Evaluation criteria:
Signal intensity at expected cellular locations
Signal-to-noise ratio
Background fluorescence levels
Staining pattern consistency with known FAR1 localization
Application-specific adjustments: Different applications may require different optimal dilutions:
Immunohistochemistry: Often requires higher concentrations
Flow cytometry: May need optimization based on expression levels
Controlling factors: Consider the degree of FITC labeling, as higher labeling indices increase sensitivity but may also increase non-specific binding
Record the fluorescein/protein (F/P) ratio of your antibody batch, as this affects optimal dilution requirements across experiments.
Research has established a clear inverse relationship between FITC-labeling extent and antibody binding performance:
| Conjugation Level | Binding Affinity | Specificity | Sensitivity | Non-specific Binding |
|---|---|---|---|---|
| Mono-conjugate | Highest (90-100%) | Highest | Lowest | Minimal |
| Di-conjugate | Moderate (50-80%) | Moderate | Moderate | Moderate |
| Tri-conjugate | Lowest (0-50%) | Lowest | Highest | Highest |
Studies with FITC-labeled proteins have demonstrated that mono-conjugated versions (with a single FITC molecule attached) typically maintain binding properties most similar to the native protein. As the number of FITC molecules increases to di- and tri-conjugates, binding affinity progressively decreases .
The position of conjugation also influences activity. For instance, studies with insulin showed that B1-position conjugation preserved biological activity, while A1-position conjugation reduced activity by 10%, and multi-site conjugation (di- and tri-) decreased activity by up to 100% .
For FAR1 antibodies, selecting conjugates with appropriate labeling indices is crucial to balance detection sensitivity with maintained target specificity.
To ensure experimental consistency, separating different FITC-conjugated antibody fractions is essential:
Gradient DEAE Sephadex Chromatography:
Principle: Separation based on charge differences from varying FITC conjugation levels
Protocol:
a) Equilibrate DEAE Sephadex column with starting buffer (typically low salt, pH 8.0)
b) Apply FITC-antibody mixture to column
c) Elute with increasing salt gradient (e.g., 0-0.5M NaCl)
d) Collect fractions and analyze for F/P ratio
Spectrophotometric Characterization:
Measure absorbance at 280nm (protein) and 495nm (FITC)
Calculate F/P ratio using established formulas:
F/P = (A495 × dilution factor) / (ε495 × [protein concentration])
where ε495 is the extinction coefficient of FITC
Validation Methods:
This separation process is critical for FAR1 antibodies to ensure consistent experimental performance across studies, especially when comparing results between different laboratories.
To evaluate potential changes in epitope recognition after FITC conjugation of FAR1 antibodies:
Comparative Binding Assays:
ELISA competitive binding: Compare IC50 values between conjugated and unconjugated antibodies
Surface Plasmon Resonance: Measure on/off rates and KD values to quantify affinity changes
Western blot analysis: Compare band recognition patterns and intensity
Epitope Mapping Approaches:
Peptide arrays: Identify specific binding regions before and after conjugation
Hydrogen-deuterium exchange mass spectrometry: Assess structural changes affecting epitope accessibility
Cross-blocking experiments: Determine if FITC-conjugated and unconjugated antibodies compete for the same binding site
Functional Assessment:
Immunoprecipitation efficiency comparison
Neutralization assays (if applicable)
Flow cytometry with comparative analysis of mean fluorescence intensity
Structural Analysis:
These methodologies provide complementary data to comprehensively evaluate whether FITC conjugation has affected the antibody's ability to recognize its target epitope on FAR1.
When incorporating FITC-conjugated FAR1 antibodies into multi-color flow cytometry panels:
Spectral Considerations:
FITC excitation maximum: ~495 nm
FITC emission maximum: ~520 nm
Potential spectral overlap with: PE, GFP, CFSE, Alexa Fluor 488
Recommendation: Perform thorough compensation using single-stained controls
Panel Design Strategies:
Assign FITC to moderately expressed antigens (not very dim antigens)
Avoid using PE-conjugated antibodies for dim antigens on the same cells
Consider brightness hierarchy when designing panels
Instrument Optimization:
PMT voltage: Optimize specifically for FITC channel
Threshold settings: Adjust to minimize debris while capturing all cells of interest
Laser alignment: Ensure proper 488nm laser functioning
Sample Preparation Considerations:
Quality Control Measures:
Include FMO (Fluorescence Minus One) controls
Monitor FITC stability throughout the experiment
Document F/P ratio of the specific antibody lot used
FITC conjugation significantly influences the permeability characteristics of antibodies:
The degree of FITC conjugation creates measurable differences in membrane permeation capacity that researchers must account for when designing transport studies with FAR1 antibodies.
A comprehensive control strategy for FITC-conjugated FAR1 antibody experiments includes:
Primary Controls for Specificity:
Isotype control: FITC-conjugated IgG of matching isotype (Rabbit IgG for FAR1 antibodies) with irrelevant specificity
Blocking control: Pre-incubation with excess unconjugated FAR1 antibody or recombinant FAR1 protein
Antigen-negative tissues/cells: Samples known to lack FAR1 expression
Antigen-positive reference: Well-characterized samples with validated FAR1 expression
Technical Controls for FITC-Specific Issues:
Unconjugated FITC control: To assess non-specific FITC binding
Autofluorescence control: Unstained samples to establish baseline fluorescence
Photobleaching control: Fixed fluorescence standard to monitor detection consistency
Procedural Controls:
No primary antibody control: To assess non-specific binding of detection systems
Concentration-matched controls: Using same protein concentration across different antibodies
F/P ratio standardization: Document and standardize fluorescein/protein ratio
Application-Specific Controls:
These controls should be systematically incorporated into experimental designs to ensure robust and interpretable results when using FITC-conjugated FAR1 antibodies.
Optimizing the F/P ratio requires a systematic approach to balance detection sensitivity with binding specificity:
Conjugation Reaction Optimization:
| Parameter | Recommended Value | Effect on F/P Ratio |
|---|---|---|
| Antibody purity | DEAE Sephadex purified | Higher purity enables more consistent conjugation |
| FITC quality | High purity (>95%) | Reduces inactive FITC molecules |
| Reaction pH | 9.5 | Maximizes reactive amine groups |
| Temperature | 25°C (room temperature) | Balances reaction rate with protein stability |
| Protein concentration | 25 mg/ml | Optimizes FITC-protein interaction |
| Reaction time | 30-60 minutes | Controls degree of labeling |
| FITC:protein molar ratio | 10:1 to 30:1 | Primary determinant of final F/P ratio |
F/P Ratio Determination Methods:
Spectrophotometric calculation: Measure A280 and A495
F/P ratio = [A495 × Dilution factor × MW of protein] ÷ [ε495 × protein concentration (mg/ml)]
For IgG antibodies, typical calculation: F/P ratio = (A495 × 0.30) ÷ A280 - (0.35 × A495)
Performance Characteristics by F/P Ratio:
| F/P Ratio | Sensitivity | Specificity | Recommended Applications |
|---|---|---|---|
| 1-2 | Lower | Highest | Quantitative analysis, critical specificity applications |
| 3-5 | Moderate | Good | Standard immunofluorescence, flow cytometry |
| 6-8 | High | Moderate | Detecting low-abundance proteins |
| >8 | Highest | Poor | Not recommended - non-specific binding issues |
Application-Specific Optimization:
The research indicates that for most applications using FAR1 antibodies, an F/P ratio of 3-5 provides optimal balance between sensitivity and specificity.
A standardized protocol for immunofluorescence with FITC-conjugated FAR1 antibodies:
Sample Preparation:
Cell fixation: 4% paraformaldehyde (10 minutes at room temperature) or cold methanol (5 minutes at -20°C)
Permeabilization: 0.1% Triton X-100 in PBS (5 minutes) for intracellular targets
Blocking: PBS containing 10% fetal bovine serum (20 minutes at room temperature)
Antibody Incubation:
Dilution: 1:500 in PBS/10% FBS (optimize based on specific antibody batch)
Incubation: 1 hour at room temperature in darkness
Washing: 3 × 5 minutes with PBS
Counterstaining and Mounting:
Nuclear counterstain: DAPI (1 μg/ml, 5 minutes)
Mounting medium: Anti-fade mounting medium to prevent photobleaching
Curing: Allow slides to set overnight at 4°C in darkness
Microscopy Parameters:
Excitation wavelength: 488 nm
Emission filter: 510-530 nm
Exposure settings: Determine optimal settings using positive control samples
Z-stack acquisition: Recommended for three-dimensional localization
Critical Considerations:
This protocol provides a foundation that can be adapted based on specific experimental requirements and cell/tissue types being examined.
Systematic troubleshooting approach for FITC-conjugated FAR1 antibody staining issues:
Weak Signal Resolution:
Increase antibody concentration (reduce dilution)
Extend incubation time (overnight at 4°C)
Enhance antigen retrieval (for tissue sections)
Check F/P ratio (should be ≥3 for standard applications)
Verify storage conditions (photobleaching or degradation issues)
Adjust microscope settings (increase exposure, gain, laser power)
Use signal amplification systems if necessary
Non-specific Staining Solutions:
Increase blocking stringency (longer time, higher serum concentration)
Add 0.1-0.3% Triton X-100 to antibody diluent
Pre-adsorb antibody with acetone powder from negative tissues
Reduce antibody concentration (increase dilution)
Check F/P ratio (>6 often increases non-specific binding)
Use antibody with optimal F/P ratio (3-5)
Include 0.05% Tween-20 in wash buffers
Pattern Inconsistency Remediation:
Standardize fixation protocols (time, temperature, fixative)
Ensure consistent permeabilization
Verify sample quality and preparation
Run parallel staining with non-conjugated FAR1 antibody plus secondary
Check for tissue autofluorescence with unstained controls
Systematic Validation Approach:
Document all troubleshooting steps and outcomes to build a laboratory-specific optimization protocol for FAR1 antibody applications.
Multiple quantification approaches are available for analyzing FAR1 expression:
Flow Cytometry Quantification:
Mean/Median Fluorescence Intensity (MFI) measurement
Molecules of Equivalent Soluble Fluorochrome (MESF) calibration
Quantitative Flow Cytometry (QFCM) using calibration beads
Fold-change relative to control populations
Fluorescence Microscopy Quantification:
Integrated density measurement (area × mean intensity)
Cell-by-cell intensity analysis with automated image processing
Nuclear/cytoplasmic ratio quantification
Colocalization coefficients with organelle markers
Plate-based Fluorescence Assays:
Microplate reader measurement of whole populations
In-Cell Western assay with normalization to cell number
High-content screening platforms for automated quantification
Standardization Approaches:
Fluorescence calibration using standard beads
Calculation of absolute number of molecules using reference standards
Normalization to housekeeping proteins
Baseline correction using isotype controls
Advanced Analysis Methods:
For accurate quantification, always include appropriate calibration standards and ensure that the detection system's dynamic range encompasses the full range of expected signal intensities.
FITC fluorescence and antibody performance vary significantly with pH, requiring careful optimization:
pH-Dependent FITC Properties:
| pH | Fluorescence Intensity | Spectral Characteristics | Stability |
|---|---|---|---|
| <6.0 | Significantly reduced | Blue-shifted emission | Reduced |
| 6.0-7.0 | Moderately reduced | Minor emission shifts | Moderate |
| 7.0-8.0 | Optimal | Standard profile (λex=495nm, λem=520nm) | Optimal |
| 8.0-9.0 | Slightly enhanced | Minor red-shifted emission | Good |
| >9.0 | Variable/quenched | Significant shifts | Poor |
Buffer System Recommendations:
Standard immunofluorescence: PBS (pH 7.4)
Flow cytometry: HEPES-buffered saline (pH 7.4)
Acidic compartment visualization: Citrate buffer (pH 5.5-6.0) with calibrated intensity correction
Alkaline phosphatase detection: Tris buffer (pH 8.0-8.5)
pH Stabilization Strategies:
Add 25mM HEPES to maintain pH during long incubations
Use anti-fade mounting media with pH buffering capacity
For live-cell imaging, use CO2-independent media with HEPES
Methodology for pH-Variable Experiments:
Create calibration curves at each experimental pH
Include pH indicators in parallel samples
Normalize fluorescence to standards at each pH
Consider alternative fluorophores (e.g., Alexa Fluor 488) for extreme pH environments
Special Considerations for FAR1 Detection:
When investigating FAR1 in cellular compartments with variable pH, these adjustments are essential for accurate quantitative and qualitative analyses.
Strategic incorporation of FITC-conjugated FAR1 antibodies into complex experimental systems:
Multi-color Microscopy Applications:
Compatible fluorophore combinations: DAPI (nuclei), TRITC/Cy3 (organelle markers), Cy5 (additional proteins)
Avoid: GFP, Alexa Fluor 488 (spectral overlap)
Sequential acquisition recommendation: Acquire FITC signal first to minimize photobleaching effects
Optimized filter sets: Use narrow bandpass filters to minimize bleed-through
Multi-parametric Flow Cytometry:
Panel design strategy: Place FITC in detector with high sensitivity
Compatible fluorophores: PE-Cy5, PE-Cy7, APC, APC-Cy7
Challenging combinations: PE, PerCP (require careful compensation)
Recommended marker allocation: Use FITC-FAR1 for moderately expressed targets
High-Content Screening Applications:
Multiplexing approach: FITC-FAR1 + compartment markers + functional indicators
Analysis strategy: Hierarchical gating based on cellular morphology → subcellular localization → FAR1 intensity
Data integration: Correlate FAR1 expression with functional readouts
Co-localization Studies:
Successful multi-parameter designs require careful consideration of spectral compatibility, antibody performance characteristics, and appropriate controls for each added parameter.
Time-course experiments with FITC-conjugated antibodies require special attention to several factors:
Photobleaching Management:
Quantification: Measure photobleaching rate under experimental conditions
Correction: Apply mathematical correction factors for quantitative analysis
Minimization: Use anti-fade reagents, reduced exposure times, and neutral density filters
Alternative approach: Consider time-lapse imaging at lower frequency with higher intensity
Sample Stability Considerations:
Temperature control: Maintain consistent temperature to prevent fluorescence intensity fluctuations
pH stability: Use buffered media to prevent pH-dependent intensity changes
Antibody internalization: Account for potential internalization and degradation of surface-bound antibodies
Fixation timing: For fixed time-points, ensure identical processing times
Experimental Design Strategies:
Internal standards: Include fluorescent beads or reference samples in each time point
Normalization approach: Express data as percent of maximum or relative to t=0
Parallel processing: When possible, process all time points simultaneously
Technical replicates: Increase replicate number for later time points to account for increased variance
Advanced Time-course Applications:
These considerations ensure accurate monitoring of dynamic changes in FAR1 expression, localization, or interaction over experimental time courses.
Systematic validation of cross-species reactivity requires multiple complementary approaches:
Sequence Analysis Foundation:
Epitope sequence alignment across species
Percent identity/similarity calculation for the FAR1 protein
Identification of conserved domains versus variable regions
Predicted antibody binding regions based on epitope mapping
Progressive Experimental Validation:
Western blot analysis: Confirm band at expected molecular weight (59 kDa) across species
Immunoprecipitation: Verify pull-down efficiency from different species lysates
Immunofluorescence: Compare staining patterns in cells from different species
Flow cytometry: Quantify binding across species-specific cell lines
Controls for Cross-reactivity Validation:
Positive control: Human samples (the established reactive species)
Negative control: Species with known sequence divergence at the epitope region
Specificity control: Competitive binding with recombinant proteins from each species
Background control: Secondary-only or isotype control for each species
Quantitative Assessment Methods:
For FAR1 antibodies specifically, reactivity has been validated in human, mouse, and rat samples, but each new lot should be tested systematically when cross-species applications are planned.
Effective multiplexing strategies for simultaneous detection of FAR1 and other targets:
Spectral Separation Approaches:
Classical multiplexing: FITC-FAR1 + spectrally distinct fluorophores (TRITC, Cy5)
Advanced spectral imaging: Linear unmixing to separate overlapping fluorophores
Sequential scanning: Minimize crosstalk between channels
Super-resolution compatibility: STED, PALM, or STORM techniques with appropriate fluorophore selection
Temporal Separation Strategies:
Sequential staining: Complete FITC-FAR1 staining before introducing additional markers
Cyclic immunofluorescence: Iterative staining-imaging-bleaching cycles
Multiplexed ion beam imaging (MIBI): Mass-based detection of multiple targets
Layer-based Approaches:
Multi-layer staining: Nuclear, cytoplasmic, and membrane markers
Z-stack analysis: 3D reconstruction to resolve spatial relationships
Tyramide signal amplification: For combining multiple antibodies from the same species
Target-specific Combinations for FAR1 Studies:
Each multiplexing approach requires careful optimization and validation to ensure that antibody binding and signal detection for each target are not compromised by the presence of additional probes.
Standardized image acquisition and analysis protocols for FITC-conjugated FAR1 antibodies:
Image Acquisition Parameters:
Excitation source: 488 nm laser or appropriate filter set (470-490 nm)
Emission filter: 510-550 nm bandpass
Exposure settings: Below saturation for brightest samples (check histogram)
Z-stack parameters: 0.5-1 μm steps depending on required resolution
Time-lapse settings: Minimum exposure to prevent photobleaching
Microscope Setup and Calibration:
Regular power calibration: Monitor laser/lamp output stability
Flat-field correction: Compensate for uneven illumination
Daily PSF measurement: Monitor system performance
Chromatic aberration correction: Critical for co-localization studies
Image Processing Workflow:
Background subtraction: Rolling ball algorithm (radius > largest object)
Deconvolution: When appropriate for confocal or widefield images
Segmentation: Thresholding based on control samples
Feature extraction: Intensity, area, shape factors, texture
Quantitative Analysis Approaches:
Single-cell analysis: Automated segmentation and intensity measurement
Subcellular localization: Co-localization with organelle markers
Population statistics: Distribution analysis across cell populations
Spatial statistics: Clustering, dispersion patterns
Standardization and Reproducibility:
These practices ensure reliable, reproducible, and quantitatively sound imaging data when working with FITC-conjugated FAR1 antibodies.