Cy5 phosphoramidite

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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-phrase	H303, H313, H333
Hazard symbol	XN
Intended use	Research Use Only (RUO)
R-phrase	R20, R21, R22
Storage	Freeze (< -15 °C); Minimize light exposure
UNSPSC	12171501

Overview SDS Protocol

Molecular weight

979.66

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

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 mg	0.5 mg	1 mg	5 mg	10 mg
1 mM	102.076 µL	510.381 µL	1.021 mL	5.104 mL	10.208 mL
5 mM	20.415 µL	102.076 µL	204.152 µL	1.021 mL	2.042 mL
10 mM	10.208 µL	51.038 µL	102.076 µL	510.381 µL	1.021 mL

Molarity calculator

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Mass (Calculate)		Molecular weight		Volume (Calculate)		Concentration (Calculate)		Moles
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Spectrum

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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

Product Family

Name	Excitation (nm)	Emission (nm)	Extinction coefficient (cm ^-1 M ^-1)	Quantum yield	Correction Factor (260 nm)	Correction Factor (280 nm)	Correction Factor (482 nm)	Correction Factor (565 nm)
Cy5 tertrazine [Cy5 tertrazine]	651	670	250000¹	0.27¹, 0.4²	0.02	0.03	0.009	0.09
Cy5 tyramide	651	670	250000¹	0.27¹, 0.4²	0.02	0.03	0.009	0.09
Cy5 tetrazine	651	670	250000¹	0.27¹, 0.4²	0.02	0.03	0.009	0.09
Cy5 aldehyde	651	670	250000¹	0.27¹, 0.4²	0.02	0.03	0.009	0.09
DBCO-Cy5	651	670	250000¹	0.27¹, 0.4²	0.02	0.03	0.009	0.09
Cy3 phosphoramidite	555	569	150000¹	0.15¹	0.07	0.073	-	-
VIC phosphoramidite	526	543	-	-	-	-	-	-

Images

Figure 1. Chemical structure for Cy5 phosphoramidite

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