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Cy3.5 (Cyanine 3.5)

Cy3.5

Code : [Cy3.5]

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picture of Cy3.5 (Cyanine 3.5)

Modification : Cy3.5

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



26-6461
Fluorescent Dyes
[Cy3.5]
Y
N
N
607.7
24
PS26-6461.pdf
588
604
150000


Catalog NoScalePrice
26-6461-0550 nmol$586.00
26-6461-02200 nmol$586.00
26-6461-011 umol$688.00
26-6461-032 umol$827.00
26-6461-065 umol$1,898.00
26-6461-1010 umol$4,218.00
26-6461-1515 umol$4,667.00
Discounts are available for Cy3.5!
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

Cyanine 3.5 (Cy3.5) is a fluorescent dye that belongs to the Cyanine family of synthetic polymethine dyes. Cy3.5 is reactive, water-soluble, and has an absorbance maximum of 581 nm and an emission maximum of 596 nm. It is available as a phosphoramidite, and is used to fluorescently label oligonucleotides at either the 5' or 3' end, or internally. Cy3.5 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, Cy3.5 is most commonly paired with the dark quencher BHQ-2, as the two have excellent spectral overlap.

Cy3 can also be used to label DNA oligos for use as hybridization probes in other applications, such as Fluorescent In-Situ Hybridization (FISH).

Applied Biosystems Proprietary Dyes & Possible Substitutions

Dye

Color

Absorbance max (nm)

Emission max (nm)

VIC Pink Red 538 554
Cal Orange 560 Pink Red 537 558
HEX Pink Red 535 556
NED Red Orange 546 575
Cy3 Red Orange 550 570
PET Red Orange 558 595
Cy3.5 Red 588 604
ROX Red 575 602
CAL Fluor Red 590 Red 569 591
Texas Red Red 583 603

Click here for a list of fluorophores.


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.
- Cy3.5 (Cyanine 3.5)

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