Cyanine 5 Phosphoramidite | CAS 351186-76-0

Cyanine 5 Phosphoramidite is a cyanine dye phosphoramidite designed for incorporation into nucleic acids during automated oligonucleotide synthesis. This dye format provides an efficient route to fluorescently labeled DNA or RNA probes and primers that are routinely used in fluorescence-based nucleic acid analysis, hybridization assays, and molecular imaging workflows where Cy5 excitation/emission compatibility is required. The phosphoramidite functionality enables controlled placement of the fluorophore within oligonucleotide constructs for downstream assay development and instrumentation-ready labeling.

1. Oligonucleotide Fluorescent Labeling

Cyanine 5 Phosphoramidite is used by molecular biology and chemical biology groups to generate Cy5-labeled DNA and RNA oligonucleotides for fluorescence detection workflows. Researchers incorporate the dye at defined positions to support consistent probe behavior in hybridization experiments, nucleic acid binding studies, and fluorescence readouts where the dye's far-red spectral region helps reduce interference from shorter-wavelength background. Common outputs include labeled primers, hybridization probes, and strand-specific reporters used in assay development for nucleic acid workflows.

2. Fluorescence Hybridization Assays

Cyanine 5 Phosphoramidite supports the construction of fluorescent hybridization probes for monitoring complementary nucleic acid binding in solution or on solid supports. In practice, Cy5-labeled oligonucleotides produced from this reagent are used for fluorescence imaging of nucleic acid targets, endpoint fluorescence assays, and probe-based detection formats where hybridization-dependent signal reporting is required. The phosphoramidite format is particularly valued when probe architecture and fluorophore placement must be controlled to maintain reliable assay performance across different target sequences and probe lengths.

3. Molecular Beacons And Stem-Loops

Cyanine 5 Phosphoramidite is also applied in the development of nucleic-acid-based fluorescent reporters such as molecular beacons and related stem-loop constructs, where a Cy5 fluorophore is incorporated into the oligonucleotide scaffold. These designs are used in research settings to translate target-dependent structural changes into fluorescence readouts, enabling real-time monitoring of nucleic acid hybridization events. By using a phosphoramidite dye building block, teams can integrate Cy5 into custom beacon architectures compatible with standard oligonucleotide synthesis workflows.

4. Fluorescent Standards For Nucleic Acid Workflows

Cyanine 5 Phosphoramidite is frequently used to prepare Cy5-labeled oligonucleotide standards and reference reagents for fluorescence-based nucleic acid measurements. Laboratories use these labeled constructs to validate imaging or plate-reader setups, calibrate fluorescence response across experiments, and standardize probe handling in assay development. This application is especially relevant when consistent fluorescent labeling and reproducible dye placement are needed to support routine method development and quality control in nucleic acid analysis.