5-Propargylamino-dCTP-Cy5 (ethyl)

5-Propargylamino-dCTP-Cy5 (ethyl) is a Cy5-labeled, nucleotide analog designed for fluorescent incorporation into nucleic acids. As a click-reactive dCTP derivative, it enables downstream conjugation or probe construction workflows while providing a strong red-emitting fluorophore handle for visualization and readout in nucleic acid assays. Researchers use this reagent to generate Cy5-tagged DNA/RNA materials for fluorescence-based detection, tracking, and quantification in molecular biology and chemical biology settings.

1. Nucleic Acid Labeling

5-Propargylamino-dCTP-Cy5 (ethyl) is used to introduce a Cy5 fluorophore into DNA or RNA during enzymatic synthesis, enabling direct fluorescence readout of labeled nucleic acid products. Molecular biology groups rely on Cy5 incorporation for imaging and quantification workflows where red fluorescence is advantageous for multiplexing or for separating nucleic acid signals from green-channel background. The propargylamino functionality provides an additional chemical handle for subsequent derivatization steps, supporting workflows that require secondary functionalization of the labeled strand.

2. Click-Functional Probe Construction

5-Propargylamino-dCTP-Cy5 (ethyl) serves as a building block for constructing click-functional nucleic acid probes and fluorescent conjugates. Chemical biology and diagnostics R&D teams incorporate the Cy5-labeled nucleotide into oligonucleotides, then use the alkyne functionality to attach the nucleic acid to complementary ligands, solid supports, or imaging scaffolds via copper-catalyzed azide-alkyne cycloaddition. This approach is commonly used when probe immobilization, multivalent display, or conjugation to other reporters is required while maintaining a robust Cy5 signal for fluorescence detection.

3. Fluorescence Hybridization Assays

5-Propargylamino-dCTP-Cy5 (ethyl) is applied in fluorescence-based nucleic acid hybridization assays where Cy5-labeled strands provide a direct measure of target binding. In research laboratories developing hybridization workflows, the Cy5 tag enables visualization of hybrid formation by fluorescence microscopy or plate-based fluorescence readers, supporting studies of nucleic acid interactions, probe performance, and workflow optimization. The click-reactive handle also allows post-synthesis tailoring of probe format, such as converting a soluble probe into a surface-associated format for assay development.

4. Flow Cytometry Oligonucleotide Tracking

5-Propargylamino-dCTP-Cy5 (ethyl) can be incorporated into labeled nucleic acid reagents used for fluorescence readout in cell-associated or particle-associated nucleic acid tracking experiments. In flow cytometry workflows, Cy5 fluorescence provides a convenient red channel signal for monitoring uptake, binding, or association of nucleic acid constructs with biological samples or engineered materials. The presence of the click-reactive functionality supports downstream conjugation strategies when researchers need to couple the nucleic acid to targeting motifs or immobilize it for controlled presentation during assay development.