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Cy5 phosphoramidite

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 Cy5 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 mM102.076 µL510.381 µL1.021 mL5.104 mL10.208 mL
5 mM20.415 µL102.076 µL204.152 µL1.021 mL2.042 mL
10 mM10.208 µL51.038 µL102.076 µL510.381 µL1.021 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

Product family

NameExcitation (nm)Emission (nm)Extinction coefficient (cm -1 M -1)Quantum yieldCorrection Factor (260 nm)Correction Factor (280 nm)Correction Factor (482 nm)Correction Factor (565 nm)
Cy5 tertrazine [Cy5 tertrazine]65167025000010.271, 0.420.020.030.0090.09
Cy5 tyramide65167025000010.271, 0.420.020.030.0090.09
Cy5 tetrazine65167025000010.271, 0.420.020.030.0090.09
Cy5 aldehyde65167025000010.271, 0.420.020.030.0090.09
DBCO-Cy565167025000010.271, 0.420.020.030.0090.09
Cy3 phosphoramidite55556915000010.1510.070.073--
VIC phosphoramidite526543------

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
Page updated on November 7, 2024

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Catalog Number6071
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Physical properties

Molecular weight

979.66

Solvent

MeCN

Spectral properties

Correction Factor (260 nm)

0.02

Correction Factor (280 nm)

0.03

Correction Factor (482 nm)

0.009

Correction Factor (565 nm)

0.09

Extinction coefficient (cm -1 M -1)

2500001

Excitation (nm)

651

Emission (nm)

670

Quantum yield

0.271, 0.42

Storage, safety and handling

H-phraseH303, H313, H333
Hazard symbolXN
Intended useResearch Use Only (RUO)
R-phraseR20, R21, R22

Storage

Freeze (< -15 °C); Minimize light exposure
UNSPSC12171501
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