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Cy5 (5'-Cyanine 5)

5'-Cy5

Code : [5-Cy5]

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picture of Cy5 (5'-Cyanine 5)

Modification : 5'-Cy5

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



26-6436
Fluorescent Dyes
[5-Cy5]
Y
N
N
533.63
250
PS26-6436.pdf
649
670
-


Catalog NoScalePrice
26-6436-0550 nmol$155.00
26-6436-02200 nmol$155.00
26-6436-011 umol$195.00
26-6436-032 umol$245.00
26-6436-065 umol$612.00
26-6436-1010 umol$1,092.00
26-6436-1515 umol$1,366.00
Discounts are available for 5'-Cy5!
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

Click here for a list of fluorophores.


Prices listed above are for 5' modification. Internal and 3' incurs additional charges and are post synthesis conjugation to a primary amino group thus an additional modification with an amino group is required. A C6 or C12 amino group can be placed at the 5' or for the 3' end a C3 or C7 amino and for internal positions an amino modified base is used, e.g Amino dT C6.


Cyanine 5 (Cy5) is a fluorescent dye that belongs to the Cyanine family of synthetic polymethine dyes. Cy5 is reactive, water-soluble, and has an absorbance maximum of 649 nm and an emission maximum of 670 nm. It is available as both a phosphoramidite and an NHS ester, and is used to fluorescently label oligonucleotides at either the 5' or 3' end, or internally. Cy5 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 is most commonly paired with the dark quencher BHQ-3, as the two have excellent spectral overlap.

Cy5 can also be used to label DNA oligos for use as hybridization probes in other applications, such as Fluorescent In-Situ Hybridization (FISH). In 2010, Stoeckler and co-workers (4) reported that Cy5 double-labeling of FISH probes (at both ends) that were specific to ribsosomal RNA targets in microorganisms at least doubles FISH signal intensity without affecting specificity. This Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) strategy may provide an effective solution to the problem of low signal intensity, which is commonly observed when using corresponding singly-labeled FISH probes for microbe identification. As an added benefit, Cy5-doubly labeled probes were shown to increase the in situ accessibility of rRNA targets sites in microbes, which allows for greater probe design flexibility.


Click here for list of quenchers.

Click here for a list of fluorophores.


Near Infrared Fluorophore Spectral Data & Quencher Selection Guide

Fluorophore Name

Excitation 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

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

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)

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