Cyanine5.5 phosphoramidite, 5'-terminal

Cyanine5.5 phosphoramidite, 5'-terminal is a cyanine dye phosphoramidite designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of a Cy5.5 fluorophore at the 5'-end of DNA or RNA. This dye platform supports fluorescence-based readouts in molecular imaging and nucleic acid assays, where spectral separation from common visible fluorophores is often used to reduce background and enable multiplexing. The phosphoramidite format is intended for straightforward conjugate construction during automated oligonucleotide assembly, producing labeled probes with defined dye placement for downstream hybridization, detection, and tracing workflows.

1. 5'-Labeled Oligonucleotide Probes

Cyanine5.5 phosphoramidite, 5'-terminal is used to generate fluorescent DNA or RNA probes with a defined 5'-Cy5.5 label for hybridization-based detection. Researchers incorporate this reagent during oligonucleotide synthesis to produce sequence-specific probes for nucleic acid analysis workflows, including probe-based binding assays and fluorescence readouts on plate readers or benchtop fluorescence instruments. The fixed dye position supports consistent labeling geometry across batches, which is particularly valuable when comparing signal intensities across probe designs or targets.

2. Fluorescence In Situ Hybridization

Cyanine5.5 phosphoramidite, 5'-terminal supports fluorescence microscopy workflows where labeled oligonucleotides are hybridized to cellular or tissue-associated nucleic acid targets. By installing the Cy5.5 fluorophore at the 5'-terminus, investigators can track hybridization localization with a far-red emitting dye that is frequently chosen to improve spectral separation from endogenous autofluorescence and other fluorophores used in multicolor imaging panels. This reagent is therefore commonly used in probe development for imaging-based nucleic acid localization studies, including microscopy experiments where dye placement and probe integrity are critical for reproducible staining patterns.

3. Nucleic Acid Hybridization Assays

Cyanine5.5 phosphoramidite, 5'-terminal is applied in fluorescence hybridization assays where Cy5.5-labeled oligonucleotides report target binding through changes in fluorescence intensity and/or hybridization-dependent signal behavior. Assay developers use the 5'-terminal label to construct detection probes for endpoint fluorescence measurements, enabling straightforward integration into custom assay formats for research and industrial R&D settings. The phosphoramidite chemistry allows the dye to be incorporated during probe synthesis, simplifying the production of labeled oligonucleotides with controlled dye stoichiometry for screening, method development, and assay optimization studies.

4. Multiplex Fluorescent Readouts

Cyanine5.5 phosphoramidite, 5'-terminal is frequently selected when multiplexed nucleic acid workflows require a far-red channel for spectral demultiplexing. Labeling the 5'-end with Cy5.5 helps investigators assign fluorescence signals to specific probe sets in panels that include multiple dyes, improving the practical usability of complex probe mixtures in imaging or fluorescence-based detection. This reagent is therefore useful for building multi-probe systems where consistent dye placement and defined oligonucleotide labeling are important for interpreting combined readouts.