Cy5.5 bis-acid

Cy5.5 bis-acid is a near-infrared cyanine dye supplied in a bis-acid form that supports water-compatible fluorescent labeling workflows while minimizing nonspecific hydrophobic interactions. Its extended conjugation provides strong fluorescence in the Cy5.5 spectral region, making it a common choice for imaging and labeling applications where reduced autofluorescence and deeper tissue penetration are advantageous. Researchers often use this dye as a labeling fluorophore for constructing fluorescent conjugates and for developing NIR fluorescence readouts in microscopy and bioassay formats.

1. Fluorescent Conjugate Labeling

Cy5.5 bis-acid is frequently used to prepare fluorescently labeled biomolecule conjugates for imaging and quantification studies, including labeling of proteins, peptides, and other research-grade ligands after attachment through appropriate coupling chemistries. In these workflows, the bis-acid character helps maintain aqueous handling for conjugate preparation and downstream assay use, while the Cy5.5 emission supports sensitive visualization with NIR-capable detectors. This dye is also used when fluorescent tagging needs to be compatible with multi-step conjugation pipelines in chemical biology and biomaterials research.

2. Near-Infrared Fluorescence Microscopy

Cy5.5 bis-acid is applied in fluorescence microscopy experiments that benefit from near-infrared signal collection, such as imaging of labeled targets in complex biological samples where visible-channel autofluorescence can interfere with interpretation. Investigators use Cy5.5-based labeling to track distribution, co-localization, and relative abundance of fluorescently tagged biomolecules in cells, spheroids, and labeled tissue preparations under NIR-capable microscope systems. The dye's spectral position supports clear separation from common background signals in many imaging setups.

3. Flow Cytometry Fluorescent Labeling

Cy5.5 bis-acid is used to generate NIR fluorescence labels for flow cytometry panels that require dyes with emission outside the typical visible range. Researchers incorporate Cy5.5-labeled conjugates into antibody or ligand labeling strategies to quantify binding to cell-associated targets and to distinguish labeled populations using NIR detection channels. This approach is particularly relevant when panel design benefits from reduced spectral overlap with standard fluorophores and when NIR readout improves background management in multi-color experiments.

4. NIR Fluorescence Bioassays

Cy5.5 bis-acid supports fluorescence-based bioassay development where near-infrared detection is used for quantifying binding, uptake, or reporter signal from fluorescent conjugates. Common applications include assay readouts that rely on NIR-compatible plate readers and imaging systems for measuring fluorescence intensity changes associated with labeled reagents. In chemical biology and biomaterials testing, Cy5.5-labeled components derived from this dye are used as quantitative reporters in workflows that require robust, instrument-friendly fluorescence detection in the Cy5.5 window.