5'-AquaPhluor^® 593 CE Phosphoramidite | CAS 2378004-17-0

5'-AquaPhluor® 593 CE Phosphoramidite is a cyanine-based fluorescent phosphoramidite designed for solid-phase oligonucleotide synthesis, enabling incorporation of the AquaPhluor 593 dye at the 5′ terminus of DNA or RNA. This reagent is used to build fluorescence-tagged nucleic acids for imaging, hybridization readouts, and fluorescence-based oligonucleotide assays, where the dye's bright emission supports sensitive visualization and quantification. The CE (controlled environment) phosphoramidite format is particularly valued in probe and primer construction workflows that require reliable dye placement at defined oligo positions.

1. Oligonucleotide Labeling

5'-AquaPhluor® 593 CE Phosphoramidite is used by molecular biology and chemical biology labs to generate 5′-labeled DNA and RNA oligonucleotides for downstream fluorescence workflows. Researchers incorporate the dye at the terminus to create defined fluorescent conjugates for binding studies, nucleic acid tracking, and assay development where dye position relative to the hybridization region is important. This format supports standardized oligo synthesis and purification strategies commonly used for probe and primer reagent preparation.

2. Fluorescent Hybridization Probes

5'-AquaPhluor® 593 CE Phosphoramidite supports the construction of fluorescence-based hybridization probes used to monitor nucleic acid binding events in solution or on solid supports. In these workflows, 5′ dye labeling provides a convenient optical handle for detecting hybridization with complementary targets using plate readers, fluorescence scanners, or gel-based fluorescence imaging. The resulting labeled probes are frequently used in nucleic acid analysis development, including assay optimization for probe concentration and hybridization conditions.

3. Nucleic Acid Sequencing Assays

5'-AquaPhluor® 593 CE Phosphoramidite is applied in nucleic acid analysis development where fluorescently labeled oligos serve as reporters for base-dependent or fragment-dependent readouts. By placing AquaPhluor 593 at the 5′ end, assay developers can design labeled primers, adapters, or sequencing-compatible oligonucleotides that produce a fluorescence signal aligned with the analytical readout. This use case is common in research settings that require reproducible fluorescent tagging of oligo components used in sequencing-adjacent workflows.

4. Fluorescent Standards And Controls

5'-AquaPhluor® 593 CE Phosphoramidite is also used to prepare fluorescent oligonucleotide standards and assay controls for method development and instrument qualification. Labs generate defined concentrations of fluorescently labeled oligos to support calibration of fluorescence detection systems and to normalize readouts across experiments. Such controls help ensure consistency when comparing fluorescence signals from different probe preparations or experimental batches in nucleic acid assays.