Bio-Synthesis offers Cy3B fluorescent dye oligonucleotide labeling. Cy3B fluorescent dye belongs to the Cyanine family of synthetic polymethine dyes. It has an absorbance maximum of 559 nm and an emission maximum of 570 nm. Cyanine dyes normally are capable of cis/trans isomerization around the polymethine, which can lead to loss of fluorescence after excitation, and weaker signal. By contrast, Cy3B is conformationally locked, the dye is not subject to photo-isomerization and improved fluorescent properties1,2. As a result, Cy3B is both extremely bright and extremely stable. Cy3B can be used to substitute in any oligonucleotide-based application suitable for Cy3, such as TaqMan probes, Scorpion primers, Molecular Beacons, or Fluorescent In-Situ Hybridization. Like Cy3, Cy3B is most commonly paired with the dark quencher BHQ-2, as the two have excellent spectral overlap.

Cy3B dye can be incorporated at any position within an oligonucleotide post-synthetically. An oligonucleotide modified with a primary amine group is used to covalently attach dye with oligonucleotide via NHS ester chemistry; other cross-linking chemistries are also available depending on particular project specifications . Dual HPLC purification is highly recommended.

Contact us for CY3B fluorescent dye oligonucleotide labeling services.

Product Information


Product Name:

Cy3B Dye Oligo Labeling


fluorescent dyes, Cyanine Dye

Modification Code:


Absorption λmax:

559 nm

Excitation (nm):


Emission (nm):


Extinction Coefficient, ε(λ):



Dual HPLC required

Delivery Format:


Shipping Conditions:

Room Temperature

Storage Conditions:

-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at -20°C) in a nuclease-free environment should be stable for years.



  1. Cooper, M., Ebner, A., Briggs, M., Burrows, M., Gardner, N., Richardson, R., West, R. Cy3B: improving the performance of cyanine dyes.J. Fluoresc. (2004), 14: 1145-150.
  2. Hall, L.M., Gerowska, M., Brown, T. A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5, and Cy3B monomers. Nucleic Acids Res. (2012), 40: e108. - Cy3B