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| Product Name | 5′-HEX (Hexachlorofluorescein) Labeled Oligonucleotide |
| Catalog No. | PRIPRO-0006 |
| Description | A custom DNA oligonucleotide with a 5′-terminal hexachlorofluorescein (HEX) fluorescent label. HEX is a green-orange fluorophore with excitation maximum at approximately 535 nm and emission maximum at 556 nm. The hexachloro substitution of fluorescein shifts the excitation and emission spectra to slightly longer wavelengths compared to FAM, enabling multiplex detection when used together with FAM-labeled oligos. The dye is conjugated via a phosphoramidite chemistry linker arm during automated synthesis. The product is HPLC purified to remove free dye and truncated sequences. Supplied as a lyophilized yellow-orange pellet in light-protective packaging with full spectrophotometric characterization. |
| Intended Use | Designed for multiplex fluorescent PCR, fragment analysis, microsatellite/STR genotyping, gene expression analysis with multiplex qPCR, and capillary electrophoresis sequencing applications requiring a second fluorescent channel. |
| Principle / Technology | Solid-phase synthesis with 5′-HEX phosphoramidite coupling; HPLC purification to ≥90% dye-labeled full-length oligonucleotide |
| Detection Method | UV-Vis spectrophotometry (A260, A535); fluorescence spectroscopy (Ex 535 nm / Em 556 nm); HPLC with dual detection |
| Sample Type | Genomic DNA for STR/microsatellite analysis; cDNA for multiplex gene expression; PCR products for fragment sizing |
| Performance Range / Specifications | 10–60 bases optimal; dye labeling confirmed by A535/A260 ratio |
| Sensitivity / LOD | Detectable at sub-nanomolar concentrations on standard fluorescence detection platforms |
| Specificity | Sequence-specific binding; spectral separation from FAM enables two-color multiplex detection |
| Reaction Conditions / Protocol | Dissolve in sterile nuclease-free water at 100 µM stock. Protect from light. Use in multiplex PCR with FAM-labeled primers at matched concentrations for balanced signal. |
| Components / Formulation | Light-protected tube with lyophilized HEX-labeled oligo; COA |
| Storage Conditions | –20 °C in light-protective container; minimize ambient light exposure |
| Shelf Life | 12 months dry at –20 °C (dark); 6 months in solution at –20 °C (dark) |
| Package Specifications | Amber tube or foil-wrapped tube; available in 5, 10, 25, or 50 nmol scales |
| Product Form | Lyophilized orange-yellow pellet |
| Quality Control | HPLC purity ≥90% full-length; MALDI-TOF MS; UV-Vis spectral scan (220–700 nm); dye-to-oligo ratio calculated from A535/A260; fluorescence emission maximum verified. |
| Key Features | Good spectral separation from FAM for two-color multiplexing; compatible with standard capillary electrophoresis filter sets; stable hexachlorofluorescein dye with reduced photobleaching; HPLC purified to remove free dye. |
| Purity | ≥90% by HPLC with fluorescence detection; single labeled species |
| Concentration | Resuspend to 100 µM based on calculated extinction coefficient; actual yield 15–40 OD260 depending on scale |
| Activity / Unit Definition | Extinction coefficient ~73,000 M⁻¹cm⁻¹ at 535 nm; quantum yield ~0.7 in aqueous buffer pH 8.0 |
| Molecular Weight | Oligonucleotide molecular weight plus approximately 590 Da for HEX linker moiety |
| Source / Origin | Synthetic oligonucleotide chemically conjugated with HEX fluorophore |
| pH Range / Optimal pH | Optimal fluorescence pH 7.5–9.0; avoid acidic conditions |
| Shipping Conditions | Ambient temperature in light-protective packaging |
| Expiration Date / Stability | 12 months at –20 °C dry in dark; 6 months at –20 °C in solution protected from light |
| Regulatory / Compliance | For research use only; not for diagnostic or therapeutic use |
| Compatibility | HEX/JOE/VIC channel on ABI 3730/3730xl, ABI 3500 series; compatible with Bio-Rad CFX96, ABI 7500, Roche LightCycler 480 HEX channel |
| Recommended Buffer System | Nuclease-free water or TE buffer pH 8.0; avoid acidic buffers |
| Application Notes / Precautions | Verify spectral separation from FAM in multiplex panels before use. For fragment analysis, prepare working dilutions fresh and protect from light. Aliquot stock solution to minimize freeze-thaw cycles. |
| Batch-to-Batch Consistency | A535/A260 ratio maintained within ±10% across synthesis batches; fluorescence emission spectrum peak within ±3 nm |
For research use only, not for clinical use.
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