Cy3.5 NHS ester is widely used in the field of biomedical research for labeling proteins, antibodies, and peptides. Its application is particularly valuable in fluorescence microscopy and flow cytometry, where it helps in visualizing and tracking biological molecules within cells and tissues. The ester group allows for efficient conjugation to primary amines, making it a popular choice for creating fluorescently tagged probes. It is also employed in molecular biology techniques such as immunofluorescence assays and in vivo imaging, providing high sensitivity and stability for detecting specific targets. Additionally, it is utilized in diagnostic applications, including the development of fluorescent biosensors and assays for disease detection.