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Cy5 azide (non-sulfonated)

Catalog No.
used for Click chemistry to label alkyne-modified oligonucleotides
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Cy5 azide is a labeling reagent ready for the use in Click Chemistry reaction which available as 10 mM solution in DMSO. For biomolecule labeling, the labeling reagent has low aqueous solubility, using of organic co-solvent to dissolve this molecular is necessary for efficient reaction. First, Cyanine dye should be dissolved in organic solvent and then added to a solution of biomolecule in appropriate aqueous buffer. Alkyne-modified biomolecules in mixtures of water with organic solvents can be labeled by Cy5 azide.

Cy5/BHQ2, which is widely used in the research, combinations on several TaqMan probes with various degree of stability of secondary structures and provides some advice on the applicability of dye/quencher pairs for DNA dual labeled probes [1].

[1] Farzan, V. M.; Aparin, I.O.; Veselova, O.A.; Podkolzin, A.T.; Shipulin, G.A.; Korshun, V.A.; Zatsepin, T.S. Cy5/BHQ dye-quencher pairs in fluorogenic qPCR probes: effects of charge and hydrophobicity. Analytical Methods, in press.

Chemical Properties

Physical AppearanceA solid
Storage24 months after receival at -20°C in the dark. Transportation: at room temperature for up to 3 weeks. Avoid prolonged exposure to light. Desiccate.
Solubility≥60.1 mg/mL in DMSO; insoluble in H2O; ≥49.1 mg/mL in EtOH with ultrasonic
Chemical Name1-(6-((3-azidopropyl)amino)-6-oxohexyl)-3,3-dimethyl-2-((1E,3E,5E)-5-(1,3,3-trimethylindolin-2-ylidene)penta-1,3-dien-1-yl)-3H-indol-1-ium chloride
SDFDownload SDF
Canonical SMILESCN1C2=CC=CC=C2C(C)(C)/C1=C\C=C\C=C\C3=[N+](CCCCCC(NCCCN=[N+]=[N-])=O)C(C=CC=C4)=C4C3(C)C.[Cl-]
Shipping ConditionShip with blue ice, or upon other requests.
General tipsFor obtaining a higher solubility, please warm the tube at 37°C and shake it in the ultrasonic bath for a while.

Spectral properties

Excitation max (nm) 646 Emission max (nm) 662
Extinction Coefficient (M-1cm-1) 250000 Quantum Yield 0.2
CF260 0.03 CF280 0.04

Quality Control

Chemical structure

Cy5 azide (non-sulfonated)

Related Biological Data

Cy5 azide (non-sulfonated)