Is Cy5 the same as 647?

Comparison between Cy5 and Alexa Fluor 647

Cy5 and Alexa Fluor 647 are both fluorescent dyes commonly used in biological and chemical research for labeling proteins, nucleic acids, and other molecules. Despite their similar applications, they are not the same compound and have distinct chemical structures and properties.

Key Differences

• Chemical Structure: Cy5 is a member of the cyanine dye family, while Alexa Fluor 647 is a sulfonated rhodamine derivative. This fundamental difference in their chemical makeup leads to variations in their spectral properties and applications.
• Spectral Properties: Both dyes are excited by red light, but their absorption and emission maxima can vary slightly. Cy5 typically has an absorption maximum around 649 nm and an emission maximum around 670 nm. Alexa Fluor 647, on the other hand, has an absorption maximum close to 650 nm and an emission maximum around 668 nm.
• Stability and Brightness: Alexa Fluor 647 is known for its enhanced photostability and brightness compared to Cy5. This makes Alexa Fluor 647 a preferred choice for applications requiring prolonged imaging or high sensitivity.
• Applications: Both dyes are used in a variety of applications, including flow cytometry, microscopy, and Western blotting. However, the choice between Cy5 and Alexa Fluor 647 may depend on the specific requirements of the experiment, such as the need for photostability or compatibility with other fluorescent dyes.

In summary, while Cy5 and Alexa Fluor 647 are used for similar purposes in research, they are distinct compounds with different chemical structures, spectral properties, and applications. The choice between them should be based on the specific needs of the research project.