Cyanine5 hydrazide | CAS 1427705-31-4

Cyanine5 hydrazide is a reactive cyanine dye designed for covalent fluorescent labeling of carbonyl-containing biomolecules through hydrazone formation. The Cy5 fluorophore provides bright far-red emission that is widely used for fluorescence imaging and fluorescence-based assays where spectral separation from green channels is advantageous. Its hydrazide functionality enables attachment to aldehydes generated on proteins, glycans, or nucleic acids, supporting downstream microscopy, flow cytometry, and conjugate tracking workflows.

1. Protein Carbonyl Labeling

Cyanine5 hydrazide is frequently used to fluorescently tag aldehyde-functionalized proteins in chemical biology and proteomics workflows. Researchers apply it to label carbonyl groups introduced by oxidation or by glycan/biomolecule derivatization, enabling visualization of protein abundance and distribution in gel-based readouts, imaging experiments, and assay development. In many labs, the far-red Cy5 signal helps reduce background from autofluorescence and supports multiplexing with green fluorophores.

2. Glycan and Sugar Tagging

Cyanine5 hydrazide is commonly incorporated into labeling strategies for glycans and carbohydrate-bearing biomolecules by coupling to aldehyde handles produced during glycan oxidation. This makes it a practical reagent for monitoring glycosylation patterns, tracking labeled glycoconjugates, and generating fluorescent standards for carbohydrate-related assays. Far-red fluorescence is particularly useful when samples contain strong intrinsic fluorescence or when co-staining with other dyes is required.

3. Nucleic Acid Aldehyde Probing

Cyanine5 hydrazide is used to label nucleic acids that have been functionalized with aldehyde groups, enabling fluorescent tracking of oligonucleotides in molecular biology workflows. Researchers employ Cy5 labeling for assay optimization, hybridization studies with fluorescent readouts, and method development where a stable far-red reporter is beneficial for instrument compatibility and reduced spectral overlap. The hydrazide reactivity provides a straightforward route to produce fluorescent nucleic acid conjugates for imaging and analytical detection.

4. Fluorescent Conjugate Tracking

Cyanine5 hydrazide supports the preparation of fluorescent conjugates used to follow biomolecule conjugation, purification, and assembly steps in research and materials development. Teams use Cy5-labeled products as tracers to confirm labeling efficiency qualitatively, monitor conjugate integrity during downstream processing, and compare batches in fluorescence-based QC workflows. The far-red emission of the Cy5 dye is especially helpful for tracking in complex mixtures where visible-channel dyes may suffer from higher background.