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AAT Bioquest

Cy3 phosphoramidite

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Physical properties
Molecular weight953.63
SolventMeCN
Spectral properties
Correction Factor (260 nm)0.07
Correction Factor (280 nm)0.073
Extinction coefficient (cm -1 M -1)1500001
Excitation (nm)555
Emission (nm)569
Quantum yield0.151
Storage, safety and handling
H-phraseH303, H313, H333
Hazard symbolXN
Intended useResearch Use Only (RUO)
R-phraseR20, R21, R22
StorageFreeze (< -15 °C); Minimize light exposure
UNSPSC12171501

OverviewpdfSDSpdfProtocol


CAS
916753-57-6
Molecular weight
953.63
Correction Factor (260 nm)
0.07
Correction Factor (280 nm)
0.073
Extinction coefficient (cm -1 M -1)
1500001
Excitation (nm)
555
Emission (nm)
569
Quantum yield
0.151
Two cyanine derivatives, Cy3 and Cy5 phosphoramidites, are the most popular fluorescent labeling reagents for preparing fluorescence-labeled oligonucleotides. Cyanine dyes are normally added once at the 5'-terminus and the MMT group should be removed on the synthesizer. The absorbance of the MMT cation (yellow) is noticeably different from the DMT cation (orange), thus the trityl absorbance can be used to monitor oligo coupling. Cyanine dye phosphoramidites have also been used successfully adjacent to the 3'-terminus. Deprotection of oligos containing cyanine dyes may be carried out with ammonium hydroxide at room temperature, regardless of the base protecting groups on the monomers used. If ammonium hydroxide is used at elevated temperature, Cy3 and Cy3.5 are more stable than Cy 5 and Cy 5.5. However, it is always prudent to use monomers with base labile protecting groups to limit the exposure time to 2 hours or less at 65°C during deprotection.

Calculators


Common stock solution preparation

Table 1. Volume of MeCN needed to reconstitute specific mass of Cy3 phosphoramidite to given concentration. Note that volume is only for preparing stock solution. Refer to sample experimental protocol for appropriate experimental/physiological buffers.

0.1 mg0.5 mg1 mg5 mg10 mg
1 mM104.862 µL524.312 µL1.049 mL5.243 mL10.486 mL
5 mM20.972 µL104.862 µL209.725 µL1.049 mL2.097 mL
10 mM10.486 µL52.431 µL104.862 µL524.312 µL1.049 mL

Molarity calculator

Enter any two values (mass, volume, concentration) to calculate the third.

Mass (Calculate)Molecular weightVolume (Calculate)Concentration (Calculate)Moles
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Spectrum


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spectrum

Spectral properties

Correction Factor (260 nm)0.07
Correction Factor (280 nm)0.073
Extinction coefficient (cm -1 M -1)1500001
Excitation (nm)555
Emission (nm)569
Quantum yield0.151

Product Family


NameExcitation (nm)Emission (nm)Extinction coefficient (cm -1 M -1)Quantum yieldCorrection Factor (260 nm)Correction Factor (280 nm)
Cy3 tetrazine55556915000010.1510.070.073
Cy3 tyramide55556915000010.1510.070.073
Cy3 aldehyde55556915000010.1510.070.073
DBCO-Cy355556915000010.1510.070.073
Cy5 phosphoramidite65167025000010.271, 0.420.020.03
VIC phosphoramidite526543----

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References


View all 1 references: Citation Explorer
Fluorescent DNA: the development of 7-deazapurine nucleoside triphosphates applicable for sequencing at the single molecule level
Authors: Seela F, Feiling E, Gross J, Hillenkamp F, Ramzaeva N, Rosemeyer H, Zulauf M.
Journal: J Biotechnol (2001): 269