5'-(5-Fluorescein) phosphoramidite | CAS 147566-42-5

5'-(5-Fluorescein) phosphoramidite is a fluorescein-labeled DNA building block used to introduce a terminal fluorescein reporter into synthetic oligonucleotides for fluorescence-based nucleic acid analysis. This phosphoramidite format integrates directly into standard solid-phase oligonucleotide synthesis workflows, enabling researchers to generate fluorescently tagged probes, primers, and molecular standards for microscopy, plate-based readouts, and nucleic-acid binding studies. The fluorescein moiety provides a widely used green emission readout that supports downstream hybridization and signal-tracking experiments.

1. Oligonucleotide Labeling

5'-(5-Fluorescein) phosphoramidite is commonly incorporated as a 5'-end fluorophore during oligonucleotide synthesis to create fluorescently labeled DNA probes for hybridization assays and nucleic acid binding experiments. Researchers use the terminal fluorescein placement to monitor probe behavior during strand annealing, wash steps, and target-dependent fluorescence changes in bench-top fluorescence readers and imaging workflows. This format is also used to prepare labeled primers for fluorescence-based nucleic acid workflows where a defined dye position is required.

2. Fluorescent Hybridization Probes

5'-(5-Fluorescein) phosphoramidite supports the construction of hybridization probes for detecting complementary nucleic acid sequences by fluorescence readout. Molecular biology groups and assay developers use fluorescein-labeled oligonucleotides to visualize binding events and to quantify hybridization in microplate assays, gel-based fluorescence imaging, and probe-target interaction studies. Terminal labeling helps maintain predictable probe architecture, which is important when comparing probe performance across sequence variants or buffer conditions.

3. FRET Pair Construction

5'-(5-Fluorescein) phosphoramidite is frequently used as the fluorescein donor component in fluorescence resonance energy transfer (FRET) probe designs where a complementary acceptor dye is introduced elsewhere in the oligonucleotide. Chemical biology and nucleic-acid diagnostics research teams leverage this donor positioning to build distance-dependent fluorescence systems for monitoring hybridization or conformational changes in labeled nucleic acid constructs. The phosphoramidite format enables straightforward incorporation into custom sequences used for FRET-based readouts.

4. Fluorescence Microscopy Standards

5'-(5-Fluorescein) phosphoramidite is applied to generate fluorescent oligonucleotide standards and labeling controls for nucleic-acid visualization experiments by fluorescence microscopy. Researchers use fluorescein-labeled DNA to validate imaging workflows, optimize staining/labeling conditions, and provide reference probes for comparing signal patterns across experimental batches. This is particularly useful in studies where labeled nucleic acids are tracked spatially on membranes, gels, or fixed sample formats.

5. Sequencing and Detection Controls

5'-(5-Fluorescein) phosphoramidite is used to prepare fluorescently tagged oligonucleotide controls that support assay development and method verification in nucleic acid workflows. Laboratories incorporate the dye-labeled oligonucleotide as a reference reagent for calibrating fluorescence-based detection instruments, checking labeling consistency, and benchmarking signal generation across experimental runs. The defined 5'-fluorescein end group helps ensure reproducible control behavior when evaluating probe designs or readout conditions.