What is the difference between Cy5 and Cy5.5?

Question

Accepted Answer

Cy5 and Cy5.5 are both cyanine dyes with several differences between them.

Basis for comparison
Cy5
Cy5.5

Type of dye
Far-red fluorophore
near-infrared (IR) fluorescence-emitting dye

Molecular weight
667.54
767.66

Molecular formula
C36H42N3BF4O4
C44H46N3BF4O4

Absorbance maximum
646 nm
675 nm

Emission maximum
662 nm
694 nm

Hydrophobicity
Highly hydrophobic
Hydrophilic due to the presence of four sulfonate groups

Applications
Used in Fluorescence Resonance Energy Transfer (FRET), Fluorescence Polarization (FP), and Time Resolved- Fluorescence Resonance Energy Transfer (TR-FRET).
Used to label DNA oligos for use as hybridization probes in other applications such as Fluorescent In-Situ Hybridization (FISH).

Basis for comparison	Cy5	Cy5.5
Type of dye	Far-red fluorophore	near-infrared (IR) fluorescence-emitting dye
Molecular weight	667.54	767.66
Molecular formula	C₃₆H₄₂N₃BF₄O₄	C₄₄H₄₆N₃BF₄O₄
Absorbance maximum	646 nm	675 nm
Emission maximum	662 nm	694 nm
Hydrophobicity	Highly hydrophobic	Hydrophilic due to the presence of four sulfonate groups
Applications	Used in Fluorescence Resonance Energy Transfer (FRET), Fluorescence Polarization (FP), and Time Resolved- Fluorescence Resonance Energy Transfer (TR-FRET).	Used to label DNA oligos for use as hybridization probes in other applications such as Fluorescent In-Situ Hybridization (FISH).

Related questions