5-Propargylamino-CTP-Cy5 (ethyl)

5-Propargylamino-CTP-Cy5 (ethyl) is a Cy5-labeled clickable nucleotide analog designed for fluorescent incorporation into nucleic acid workflows. The molecule combines a CTP-derived recognition handle with a terminal propargyl (alkyne) functionality, enabling copper-catalyzed azide-alkyne cycloaddition after uptake or during post-synthetic conjugation strategies. Cy5's red emission supports fluorescence microscopy and fluorescence-based nucleic acid analysis formats where bright, long-wavelength readout is advantageous.

1. Nucleic Acid Click Labeling

5-Propargylamino-CTP-Cy5 (ethyl) is used to generate fluorescently traceable RNA or DNA materials that can be further functionalized through click chemistry. Researchers incorporate the Cy5-tagged CTP analog into nucleic acid constructs, then use the alkyne handle to couple additional probes, affinity tags, or imaging moieties via azide-bearing partners. This approach supports workflows where a nucleic acid scaffold needs both intrinsic Cy5 fluorescence and orthogonal modular attachment for downstream assays, such as building multicomponent hybridization probes or labeling libraries for microscopy and fluorescence imaging.

2. Fluorescent RNA Transcription Probes

5-Propargylamino-CTP-Cy5 (ethyl) is commonly applied in fluorescence-based RNA detection and visualization by producing Cy5-containing RNA transcripts. Molecular biology teams use the Cy5 signal to track hybridization events, monitor transcription-derived RNA probes, and visualize nucleic acids in imaging experiments. The propargyl group provides a convenient secondary attachment site for adding capture handles or secondary reporters, enabling probe customization for nucleic acid hybridization workflows and nucleic acid staining strategies that benefit from red fluorescence.

3. Click-Functional Nucleic Acid Conjugates

5-Propargylamino-CTP-Cy5 (ethyl) supports the construction of nucleic acid conjugates for advanced molecular imaging and analytical reagent development. After Cy5 incorporation, the alkyne functionality enables attachment of azide-bearing ligands such as cell-targeting motifs, surface-binding groups for immobilization, or fluorophore/quencher components for ratiometric or multiplex readouts. This makes the reagent useful for building custom fluorescent nucleic acid tools used in assay development, including probe immobilization on surfaces and preparation of multicolor nucleic acid reagents for fluorescence microscopy and plate-based fluorescence measurements.

4. Multiplex Fluorescence Hybridization Assays

5-Propargylamino-CTP-Cy5 (ethyl) is leveraged in multiplex nucleic acid analysis where a Cy5 channel is paired with other fluorescent labels or reporters. The Cy5 component provides a robust red fluorescence readout for hybridization-dependent signals, while the clickable propargyl functionality allows additional reporter placement to support assay architectures that require modular probe design. Researchers use these capabilities to tailor nucleic acid probes for multi-target experiments and to streamline development of fluorescence-based nucleic acid workflows that rely on click-compatible probe engineering.