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Oligo Modifications List | Oligo Modifications Reference Category
Modification : Cy5
Reference Catalog Number 26-6436
Category Fluorescent Dyes
Modification Code Cy5
5 Prime Y
3 Prime Y
Internal Y
Molecular Weight (mw) 533.63
Extinction Coeficient (ec) 10
Technical Info (pdf) PS26-6436.pdf
Abvsorbance MAX 649
Emission MAX 670
Catalog NoScalePrice
26-6436-0550 nmol$90.00
26-6436-02200 nmol$90.00
26-6436-011 umol$117.00
26-6436-032 umol$175.50
26-6436-1010 umol$936.00
26-6436-1515 umol$1,171.00

Discounts are available for 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

Related Modifications
Cy5 disulfo NHS
Cy3
Cy2 NHS
Cy5.5
Cy7 NHS
Cy3 NHS
Cy3.5
Cy3B
Cy5
Cy5 NHS

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.

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.
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