Cy5.5 (Cyanine 5.5)

Cy5.5

Code : [Cy5.5-5]

Modification : Cy5.5

Catalog Reference Number
Category
Modification Code
5 Prime
3 Prime
Internal
Molecular Weight (mw)
Extinction Coeficient (ec)
Technical Info (pdf)
Absorbance MAX
Emission MAX
Absorbance EC

26-6460
Fluorescent Dyes
[Cy5.5-5]
Y
N
N
633.74
21.5
PS26-6460.pdf
684
710
-

Catalog No	Scale	Price
26-6460-05	50 nmol	$586.00
26-6460-02	200 nmol	$586.00
26-6460-01	1 umol	$688.00
26-6460-03	2 umol	$827.00
26-6460-06	5 umol	$1,898.00
26-6460-10	10 umol	$4,218.00
26-6460-15	15 umol	$4,667.00

Discounts are available for Cy5.5!
Modification* Discount Price Structure
1 site/order	List price
2 sites/order	10% discount
3 sites/order	20% discount
4 sites/order	30% discount
5-9 sites/order	50% discount
10+ sites/order	60% discount
*Exceptions apply

Related Modifications
Cy5 disulfo NHS	Cy3.5 Internal	Cy3-5'
Cy7 NHS	Cy2 N	Cy5.5
Cy5.5-Internal	Cy5 NHS	Cy5-5'
Cy3B-N	Cy5 Internal	Cy3.5-5'
Cy3 NHS	Cy3 Internal

Cyanine 5.5 (Cy5.5) is a far-red/near infra red (NIR) fluorescent dye that belongs to the Cyanine family of synthetic polymethine dyes. Cy5.5 is reactive, water-soluble, and has an absorbance maximum of 675 nm and an emission maximum of 694 nm. It is available as a phosphoramidite, and is used to fluorescently label oligonucleotides at either the 5' or 3' end, or internally. Cy5.5 plays a particularly important role in real-time PCR applications, being used as a reporter moiety in TaqMan probes (1), Scorpion primers (2) and Molecular Beacons (3). For such probes, Cy5.5 is most commonly paired with the dark quencher BHQ-3, as the two have excellent spectral overlap.

Cy5.5 can also be used to label DNA oligos for use as hybridization probes in other applications, such as Fluorescent In-Situ Hybridization (FISH).

Near Infrared Fluorophore Spectral Data & Quencher Selection Guide
Fluorophore Name	Absorbance Max, nm +/-10	Emission Max, nm +/-10	Extinction Coefficient*	Color**	Quencher
Cy5	650	665	250,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 650 NHS	650	665	230,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
AZ647 NHS	655	680	191,800	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
AZ680 NHS	678	701	185,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Cy5.5	684	710	198,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 700 NHS	684	710	288,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
AZdye700 NHS	696	719	192,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Atto 700 NHS	700	716	120,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Atto 725 NHS	728	751	120,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Atto 740 NHS	743	763	120,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Cy7 NHS	740	773	199,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 750 NHS	756	776	260,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
cy7.5 NHS	788	808	223,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 800 NHS	795	819	240,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
* Extinction coefficient at λ (max) in cm-1M-1. Typical emission color seen through the eyepiece of a conventional fluorescence microscope with appropriate filters. Near-IR region. Human vision is insensitive to light beyond ~650 nm; it is not possible to view near-IR fluorescent dyes. Click here for a list of fluorophores.**
Click here for list of quenchers.

References
1. Livak, K.J., Flood, S.J.A., Marmaro, J., Giusti, W., Deetz, K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization.PCR Methods Appl. (1995), 4: 1-6.
2. Thelwell, N., Millington, S., Solinas, A., Booth, J., Brown, T. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. (2000), 28: 3752-3761.
3. Tyagi, S., Kramer, F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. (1996), 14: 303-308.
4. Stoecker, K., Dorninger, C., Daims, H., Wagner, M. Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility. Appl. Environ. Microb.. (2010), 76: 922-926.
- Cy5.5 (Cyanine 5.5)