Product manual
Product use, preparation, operating conditions and storage.
Cy3.5Reactive dye
Cy3.5 Azide
Cat. No.QH-30-3002(Azide)
Couple to a matched alkyne: terminal alkynes use CuAAC, while strained alkynes use copper-free SPAAC.
Packs & quoteCuAAC · Cu(I)-catalyzed
N₃
Azide dyeR–C≡CH
Terminal alkyneTriazole
Covalent linkageSPAAC · Copper-free
N₃
Azide dyeR–DBCO
Strained alkyneTriazole
Covalent linkageExcitation591 nm
Emission604 nm
TargetTerminal alkynes or suitable strained alkynes such as DBCO and BCN
Azide–alkyne cycloaddition
An azide dye does not directly label ordinary primary amines or thiols. Identify the target alkyne before choosing copper-catalyzed or strain-promoted cycloaddition.
Modified nucleic acids and peptides
Use a suitable CuAAC system for terminal-alkyne samples, removing free dye and catalyst components during purification.
Strained-alkyne-modified samples
Pair with DBCO or BCN for copper-free coupling after removing competing free reagents.
Multicolor channels and near-infrared detection
Check the light source, filters and detector response against this catalog number’s wavelengths. For near-infrared forms, check detector sensitivity in that range; use separate single-color controls for adjacent Cy channels.
Specifications
Product information
- Product name
- Cy3.5 Azide
- Cat. No.
- QH-30-3002(Azide)
- Product form
- Azide
- Target
- Terminal alkynes or suitable strained alkynes such as DBCO and BCN
- Pack sizes
- 1 mg / 5 mg / 10 mg / 25 mg / 100 mg
Preparation and properties
- Excitation wavelength
- 591 nm
- Emission wavelength
- 604 nm
- CAS
- 3077081-53-6
- Molar extinction coefficient
- 116,000 M⁻¹ cm⁻¹
- Quantum yield
- 0.35
- Storage
- Store at -20°C, protect from light and moisture
Spectral information and detection
Product parameters
Use parameters for the exact catalog number when preparing reagents, setting reagent input or calculating results. Request a lot-specific CoA for test results.
Protocol
Confirm the reaction pair
Record the alkyne, handle count and modification method. Ordinary terminal alkynes do not use the same copper-free conditions as DBCO.
Catalyst compatibility
For CuAAC, assess copper, ligand and reducing-system effects on the sample and readout. For SPAAC, check strained-alkyne stability and residual free handles.
Choose the route
Choose a validated system for the terminal or strained alkyne and include a no-alkyne control.
Run a small-scale reaction
Match solvent fractions and compare input and time. Control catalyst components for CuAAC; do not add copper to a copper-free reaction.
Purification and analysis
Select desalting, size-exclusion separation, dialysis or chromatography for the sample size. Remove free reagent before measuring concentration, labeling density and function. Residual free dye raises background and biases labeling-density calculations.
Confirm conjugation and function
Confirm the product by chromatography, electrophoresis, mass spectrometry or another suitable analysis rather than inferring conversion from total fluorescence.
Request product documentation
Select a document and enter your phone and email. Include the lot number for a CoA.
Cy3.5 AzideQH-30-3002(Azide)
Spectra and measurement conditions
Spectra, measurement conditions and detection settings for the exact catalog number.
Certificate of analysis (CoA)
Lot-specific test results. Include the lot number from the vial.
Safety data sheet (SDS)
Handling, storage and emergency response information.
Quality and lot information
No-alkyne control
An identically handled sample without an alkyne reveals adsorption and free-dye background.
Catalyst dependence
For CuAAC, include appropriate no-copper or no-ligand controls. For SPAAC, compare handle-positive and handle-negative samples under matched conditions.
Input titration
Compare a molar input series and assess signal, negative background, product recovery and function together.
Concentration and self-quenching
Excessive dye loading can cause self-quenching in protein conjugates. Compare purified conjugates made at lower inputs using equal protein amounts and common acquisition settings, assessing signal, background and binding rather than compensating for weak signal by adding more dye.
Technical articles
Application support
Include your sample, formulation and detection method when requesting application guidance.
References
Anomalous fluorescence enhancement of Cy3 and cy3.5 versus anomalous fluorescence loss of Cy5 and Cy7 upon covalent linking to IgG and noncovalent binding to avidin
Gruber HJ, Hahn CD, Kada G, et al. · Bioconjugate Chemistry · 11(5):696–704 · 2000
Compares fluorescence changes when Cy3, Cy3.5, Cy5 and Cy7 associate with IgG or avidin, informing joint assessment of labeling density and the purified conjugate’s signal.
DOI: 10.1021/bc000015m
Copper-Catalyzed Azide–Alkyne Click Chemistry for Bioconjugation
Presolski SI, Hong VP, Finn MG. · Current Protocols in Chemical Biology · 3(4):153–162 · 2011
Describes CuAAC catalyst systems and reaction assessment for terminal-alkyne substrates.
A Strain-Promoted [3 + 2] Azide–Alkyne Cycloaddition for Covalent Modification of Biomolecules in Living Systems
Agard NJ, Prescher JA, Bertozzi CR. · Journal of the American Chemical Society · 126(46):15046–15047 · 2004
Introduces ring-strain-driven azide–alkyne coupling without copper, a foundational study in SPAAC bioconjugation.
DOI: 10.1021/ja044996f
Frequently asked questions
Can an azide directly label an antibody?
The antibody needs a suitable alkyne handle. Native amines and thiols do not substitute for a click handle.
Is copper always required?
Terminal alkynes normally use CuAAC; strained alkynes such as DBCO and BCN can use SPAAC. The paired handle determines the route.
Does high fluorescence mean complete reaction?
Total fluorescence includes free dye and adsorption. Purify and characterize the product before evaluating conversion.
Can Cy reactive forms share one parameter set?
Check wavelengths, solvent, molecular weight and correction data by catalog number. Reactive forms sharing a dye name can differ; retain the exact catalog number during selection and comparison.