6-Tetrachloro-Fluorescein Phosphoramidite | CAS 877049-90-6

6-Tetrachloro-Fluorescein Phosphoramidite is a fluorescein-based phosphoramidite designed for incorporation into nucleic acids during automated oligonucleotide synthesis, enabling fluorescent labeling with a dye that is well-established in fluorescence imaging and nucleic-acid workflows. The tetrachloro-substituted fluorescein scaffold provides a strong fluorescence signal suitable for probe construction, while the phosphoramidite functionality supports direct synthesis-compatible attachment to DNA or RNA strands for downstream hybridization and detection experiments.

1. Oligonucleotide Fluorescent Labeling

6-Tetrachloro-Fluorescein Phosphoramidite is used by molecular biology and chemical biology groups to generate fluorescently labeled oligonucleotides for hybridization-based assays, nucleic acid tracking, and probe development. Researchers incorporate the phosphoramidite at defined positions within DNA or RNA sequences to create sequence-specific fluorescent reporters for monitoring binding events, strand displacement workflows, or target-dependent fluorescence readouts in plate-based assays and benchtop fluorescence measurements. This reagent is particularly valuable when positional control of the dye within the oligo is required to tune labeling density and performance in downstream hybridization experiments.

2. Molecular Beacon Probe Construction

6-Tetrachloro-Fluorescein Phosphoramidite supports the assembly of fluorescent molecular beacons and related hairpin probes where a fluorescein signal is used as the optical readout for target-induced conformational changes. By installing the dye directly into the oligonucleotide backbone via phosphoramidite chemistry, probe developers can build beacon formats for real-time monitoring of nucleic acid hybridization in solution, including workflows that rely on fluorescence changes upon target binding. This approach is commonly used in nucleic acid analysis development, where reproducible probe synthesis and defined dye placement are critical for consistent assay behavior.

3. Fluorescent FRET Pair Building

6-Tetrachloro-Fluorescein Phosphoramidite is frequently employed as the fluorescein donor component in FRET-based nucleic acid systems, including hybridization probes and strand-displacement reporters. Probe designers incorporate the fluorescein phosphoramidite into one oligonucleotide strand and pair it with an appropriate acceptor dye on a complementary strand or quencher-bearing oligo to create distance-dependent fluorescence responses. Such FRET architectures are used in fluorescence-based nucleic acid detection and assay development where controlled signal modulation is required to translate hybridization events into measurable optical changes.

4. Nucleic Acid Hybridization Assays

6-Tetrachloro-Fluorescein Phosphoramidite enables fluorescent readouts in nucleic acid hybridization experiments, including probe-based detection formats used for research assays and analytical method development. Fluorescein-labeled oligonucleotides prepared with this reagent are used to visualize and quantify hybridization in gel-based workflows, microarray-style experiments, and solution-phase binding studies where fluorescence intensity reports on target binding. The phosphoramidite format allows straightforward integration into custom sequences, supporting assay optimization for different target lengths and hybridization conditions.

5. Fluorescence Microscopy of Labeled Oligos

6-Tetrachloro-Fluorescein Phosphoramidite is used to create fluorescently labeled DNA or RNA probes for fluorescence microscopy applications in molecular imaging workflows. Researchers incorporate the dye into oligonucleotides used for in situ hybridization-style experiments, nucleic-acid localization studies, or fluorescence-based visualization of specific nucleic acid sequences in fixed sample formats. Defined dye placement via phosphoramidite synthesis supports consistent probe performance across experiments and helps enable multiplexed imaging strategies when paired with other spectrally distinct labels.