CY7 DBCO chloride , CAS No.C1449679

CAS: C1449679 Cat. No.: C1449679 Formula: C₅₂H₅₅ClN₄O₂ Peso molecolare: 803.47

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Panoramica

CY7 DBCO chloride is a dye derivative of CY7 bearing a DBCO group. CY7 DBCO chloride is a click chemistry reagent. CY7 DBCO chloride contains a DBCO group that can undergo strain-promoted alkyne-azide cycloaddition (SPAAC) with molecules containing Azide groups.

Specifications

Condizioni di conservazione di stoccaggio

Store at -20°C

Spedito in

Ice chest + Ice pads

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Nomi e identificatori

• Peso molecolare: 803.47

Application Protocols

General workflow for SPAAC labeling with CY7 DBCO chloride (guidance only; adapt to your system):

Stock preparation:

• Equilibrate vial to RT in the dark. Dissolve dye in anhydrous DMSO to 5–10 mM. Vortex gently; protect from light.

Protein/biomolecule labeling (azide-functionalized):

• Buffer: 50 mM phosphate or HEPES, 150 mM NaCl, pH 7.2 (no sodium azide). Optional 0.01% Tween‑20.
• Mix substrate at 10 µM with dye at 20–50 µM (2–5 equivalents per azide site or per mole of protein if single-site azide).
• Incubate 30–120 min at 20–25°C, protected from light. Gentle mixing suffices.
• Quench/cleanup: Desalt using spin columns (e.g., 7 kDa MWCO) or SEC. Collect labeled fraction.

Small-molecule/peptide labeling:

• Use equimolar to 1.5× dye in mixed aqueous/organic media (e.g., 50% buffer/50% DMF). Monitor by LC–MS. Purify by RP-HPLC.

Quality control:

• Record UV–Vis spectrum; verify Cy7 absorbance peak. Determine labeling efficiency by Amax/A280 for proteins using dye-specific extinction and correction factors (item-specific values not provided here).
• Confirm absence of free dye by SEC or analytical HPLC.

Storage of solutions:

• Aliquot stocks (e.g., 100–500 µL) in amber vials at −20°C. Avoid repeated freeze–thaw. Use within a few weeks for best performance.

Note: Exact extinction coefficients, correction factors, and stability data are Not specified for this item; consult CoA/Spec Sheet.

Biological Roles

This product is a synthetic fluorophore conjugation reagent and has no endogenous biological role. The following refers to general properties of Cy7-class dyes and DBCO conjugation in biochemical research (not clinical use):

• Fluorophore characteristics (literature): Cy7 is a near-infrared heptamethine cyanine dye with typical absorption around 740–760 nm and emission around 770–800 nm, enabling low-background detection in complex biological matrices due to reduced autofluorescence and deeper optical penetration in tissues (instrumentation- and medium-dependent).
• Conjugation chemistry: The DBCO motif reacts selectively and bioorthogonally with azide groups on biomolecules via SPAAC, forming a stable triazole linkage without catalysts, compatible with live-cell labeling workflows that introduce azides metabolically or via chemical modification.
• Applications in biochemistry: Creation of fluorescent probes, labeling of proteins/antibodies for spectroscopy and imaging, FACS panel extension into NIR channels, nucleic acid labeling for gel/CE detection, and tracking of glycan/lipid metabolic incorporation using azido-precursors. These are research-only workflows.
• Photophysics in biological media: Cyanines can show environment-sensitive quantum yields and lifetimes; binding to proteins or membranes often increases brightness and photostability. Aggregation can quench signal; using low micromolar concentrations and modest organic cosolvent reduces this.
• Quenching/energy transfer: Cy7 frequently serves as an acceptor in FRET pairs with donors like Cy5.5/Alexa 680 family, facilitating distance measurements and biosensor design (general literature guidance).

Item-specific biocompatibility, toxicity, and extinction/quantum yield: Not specified for this item; consult SDS and CoA.

Buffer Applications

This product is not a buffering reagent. It is a fluorescent labeling dye intended for SPAAC conjugation.

Practical buffer guidance for labeling (general, non-item-specific):

• Preferred reaction buffers: Phosphate (PBS), HEPES, or citrate at pH 6.5–7.5. Avoid primary amine-containing buffers (e.g., Tris) during coupling if they interfere with downstream analyses, though SPAAC itself is generally tolerant.
• Ionic strength: 50–200 mM salt often helps maintain protein stability; adjust as required for your biomolecule.
• Additives: 0.01–0.1% non-ionic detergents (Tween‑20) may limit dye aggregation; 1–5% glycerol can aid protein stability. Keep organic cosolvent (DMSO/DMF) ≤10% v/v.
• Metal ions: Not required (copper-free). Avoid azide salts in buffers (e.g., sodium azide as preservative) during reaction; azide will consume DBCO.

If you need a true buffer system recommendation for pH control, select from standard biological buffers (phosphate, HEPES, MOPS) appropriate to your biomolecule; this dye itself does not define buffer capacity.

Green Alternatives

Greenness considerations for CY7 DBCO chloride revolve around solvent choice, conjugation chemistry, and workup, not the chromophore itself.

• Copper-free advantage: SPAAC avoids Cu(I) catalysts required for classical azide–alkyne cycloaddition (CuAAC), eliminating copper waste and post-reaction metal removal steps—beneficial for biomolecule integrity and EHS profiles (literature/general).
• Solvent selection: Prefer water-rich media with minimal DMSO/DMF cosolvent (<10% v/v) where solubility allows. For process-scale surface labeling, consider bio-based solvents (e.g., Cyrene or 2-MeTHF) for intermediate handling, validating dye stability first.
• Energy and light: Perform reactions at ambient temperature and protect from light to reduce energy usage and degradation.
• Purification: Employ aqueous SEC or centrifugal desalting over extensive organic chromatography to lower solvent consumption.

Comparison (general; not item-specific):

• SPAAC with DBCO vs CuAAC with terminal alkyne
  • Catalyst: None vs Cu(I) (often with ligands)
  • Biocompatibility: High vs Moderate (copper sensitivity)
  • Waste: Lower metal waste vs Copper-containing waste
  • Kinetics: Moderate-fast at RT vs Fast with optimized ligands

Alternative fluorophores:

• Consider sulfonated Cy7–DBCO analogs for better water use (reduced organic cosolvent need) or shorter-wavelength dyes (e.g., AF647 derivatives) if instrumentation favors them. Trade-offs include brightness, photostability, and spectral overlap.

Note: Item-specific stabilizers, solvent restrictions, or green certifications are Not specified for this item; refer to CoA/Spec Sheet.

Pharmaceutical Uses

No therapeutic or clinical claims are made for this product. CY7 DBCO chloride is supplied strictly for research and laboratory use.

Relevant non-clinical/formulation roles (general):

• Developmental tool compound for assay and device calibration in the near‑IR spectral region (e.g., instrument performance checks, optical phantoms) in R&D settings.
• Conjugation handle for creating analytical reference materials (fluorescently tagged peptides/proteins/oligonucleotides) used in process development and in vitro diagnostics research. Any use in regulated workflows requires independent qualification.
• Material science/biomaterials: Fluorescent tagging of polymers, nanoparticles, or surfaces via azide handles to study coating uniformity, diffusion, and release profiles (research only).

Pharmacopeial status, impurity limits, and excipient monographs: Not specified for this item; refer to CoA/Spec Sheet. If use in GMP or diagnostic manufacturing is contemplated, request comprehensive documentation (CoA, stability data, impurity profiles) and perform internal qualification and risk assessment.

Note: For any work near clinical or manufacturing environments, ensure dye leachables/extractables, residual solvents, and counterions meet your internal specifications—these parameters are not provided here and must be established by the end user.

Physical Properties

Item-specific physical properties (from Product Data):

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

Common/literature properties for Cy7-class DBCO dyes (for general reference only; not specifications for this item):

• Absorption/emission (Cy7 core, typical): λabs ≈ 740–760 nm; λem ≈ 770–800 nm, depending on substituents, solvent, and environment.
• Molar extinction coefficient (Cy7 family): often 200,000–250,000 M−1 cm−1 (literature range; specific value depends on exact structure).
• Quantum yield: typically low-to-moderate in aqueous buffer (e.g., 0.05–0.2), higher in less polar or protein-bound environments (literature generality).
• Solubility: Many DBCO–Cy7 constructs are sparingly soluble in pure water and readily soluble in anhydrous DMSO and DMF; aqueous work often uses ≤10% DMSO cosolvent or surfactants (literature practice).
• Aggregation: Cyanines can form H/J aggregates in water and at higher concentrations, altering spectra; adding mild organic cosolvent, protein, or detergents reduces aggregation (general observation).
• Stability: Light- and oxygen-sensitive; photobleaching can occur under high-intensity illumination. Store under inert atmosphere and protect from light (general best practice).

Measured item-specific values such as melting point, density, refractive index, logP, pKa, H2O content, residual metals, or UV cutoffs: Not specified for this item; refer to CoA/Spec Sheet.

Quality and Grades

Item-specific grade/purity (from Product Data):

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.

How to interpret grades for labeling dyes (general guidance):

• “Labeling grade” or “bioconjugation grade” typically indicates high chemical purity and low levels of reactive impurities (amines, acids, metals) that can interfere with coupling or fluorescence.
• “HPLC-purified” suggests the dye is purified by preparative HPLC and often accompanied by chromatographic purity (e.g., >90–95%) on CoA. Low levels of geometric isomers and side products improve spectral consistency.
• Counterion and salt form: The chloride salt implies the dye is supplied as a cationic species neutralized by Cl−; counterion identity can influence solubility and chromatographic behavior.
• Stabilizers: Some cyanine dyes include trace stabilizers or are lyophilized with bulking agents to enhance shelf life. Presence/absence for this item: Not specified for this item; refer to CoA/Spec Sheet.

What to check on receipt (best practice):

• Verify chromatographic purity and identity via HPLC/LC–MS per CoA.
• Inspect absorbance/emission spectra in intended buffer to confirm expected maxima for Cy7-class dyes.
• Confirm residual solvent, water content, and counterion via Karl Fischer, GC, or ion chromatography as needed (not provided here; consult CoA).

If grades suitable for GMP or diagnostic manufacturing are required, request documentation (CoA, CoO, TSE/BSE statements) specific to the lot.

Reaction and Applications

Primary application: Copper-free click labeling of azide-functionalized targets via strain-promoted azide–alkyne cycloaddition (SPAAC), appending a near‑IR Cy7 fluorophore.

Use cases (research/lab):

• Bioconjugation to azide-bearing antibodies, proteins, peptides, nucleic acids, glycans, lipids, and surfaces without copper catalysts, suitable for live-cell compatible workflows (no copper toxicity) and for delicate biomolecules.
• Multiplex imaging and flow cytometry panels where a Cy7 channel is available; near‑IR emission reduces autofluorescence (instrument-dependent; general observation).
• Tracking, biodistribution studies in model systems, and probe development for assays requiring NIR readouts (non-clinical, research only).

Mechanistic notes (literature):

• SPAAC proceeds via concerted [3+2] cycloaddition of the azide 1,3-dipole with the strained alkyne in DBCO to form a stable triazole, typically without side reactions or catalysts.
• Reaction kinetics depend on solvent, temperature, and substituents; DBCO–azide second-order rate constants commonly 0.1–1 M−1 s−1 at room temperature in aqueous-organic media.

Practical tips:

• Prepare fresh, anhydrous DMSO stock; protect from light. Minimize exposure to nucleophiles that could degrade cyanine.
• For proteins, use pH 6.8–7.5 buffers lacking primary amines (avoid Tris during coupling); phosphate, HEPES, or PBS are typical. Add dye last to reduce local over-labeling.
• Typical dye-to-azide stoichiometry: 1.1–5.0 equivalents of dye relative to azide sites, depending on desired degree of labeling and substrate accessibility.
• Remove excess dye by desalting (NAP-5), spin columns (MWCO), SEC, or dialysis. Verify labeling by absorbance ratio (Amax,dye/A280) and, if applicable, MS.

Manufacturer Applications: Not provided in Product Data; the above expands on the standard SPAAC use of DBCO–Cy7 reagents.

Reaction Conditions

General SPAAC labeling conditions for DBCO–Cy7 reagents (literature guidance; not item-specific specifications):

• Substrates: Azide-functionalized biomolecules (proteins, antibodies, peptides, oligos), polymers, or surfaces.
• Solvent system: Aqueous buffers (PBS, HEPES, pH 6.8–7.5) with 1–10% DMSO or DMF to solubilize dye. Avoid sodium azide preservative during coupling.
• Temperature: Ambient (20–25°C). Lower temperatures (4–8°C) slow reaction; higher temperatures may increase dye degradation/bleaching.
• Concentrations: Biomolecule 1–50 µM typical for proteins; dye stock 1–10 mM in anhydrous DMSO. Final dye equivalents 1.1–5× per azide site. For small molecules, equimolar to slight excess dye.
• Time: 15 min to 2 h for many systems; sterically hindered or low-azide-density substrates may require 4–16 h.
• Kinetics: Second-order rate constants for DBCO–azide 0.1–1 M−1 s−1 at RT in mixed aqueous/organic media (literature range).
• Quenching/cleanup: After completion, dilute and purify by SEC, desalting, dialysis (proteins), or RP-HPLC (small molecules/peptides). Additives like 0.01–0.05% Tween‑20 can reduce adsorption losses.
• Analytical verification: Record UV–Vis spectrum (expect Cy7 maxima ~740–760 nm) and fluorescence emission (~770–800 nm). For proteins, calculate degree of labeling (DOL) using absorbance at Amax and A280 with appropriate correction factor; determine by MS when feasible.

Item-specific optimal pH, buffer composition, extinction coefficient, and correction factors: Not specified for this item; refer to CoA/Spec Sheet.

Safety and Handling

Authoritative safety information must be taken from the product SDS.

Item-specific hazard data (from Product Data):

• GHS Classification: Not specified for this item; refer to SDS.
• Signal word: Not specified for this item; refer to SDS.
• H‑statements and pictograms: Not specified for this item; refer to SDS.

General safety considerations for cyanine dyes bearing DBCO (literature/general):

• Likely hazards: May cause skin/eye/respiratory irritation; DBCO is a strained alkyne and can react with azides; avoid contact with sodium azide solutions unless intentional SPAAC labeling is intended.
• Light sensitivity: Protect solids and solutions from light to minimize photodegradation and photobleaching.
• Handling: Work in a chemical fume hood. Wear appropriate PPE: lab coat, safety glasses, and nitrile gloves. Use amber vials and foil wrap for solutions.
• Incompatibilities: Strong oxidizers and strong acids/bases may degrade the polymethine chain. Avoid prolonged exposure to aqueous media at high pH (>9) where hydrolysis/bleaching can accelerate.
• First aid (overview; defer to SDS):
  • Skin/eye contact: Rinse with water for ≥15 minutes; remove contaminated clothing; seek medical advice if irritation persists.
  • Inhalation: Move to fresh air; seek medical attention if symptoms occur.
  • Ingestion: Rinse mouth; do not induce vomiting; seek medical attention.
• Spill/cleanup: Avoid dust/aerosol formation. Absorb solutions with inert material; dispose per institutional and local regulations.
• Fire safety: Combustible organic; use CO2, dry chemical, or foam. Combustion may produce CO/CO2 and nitrogen-containing fumes.

Always consult the SDS for definitive hazard classification and response measures.

Solvent Selection

Solubility expectations (general for Cy7–DBCO constructs):

• Primary solvents: Anhydrous DMSO or DMF typically give clear, high-concentration stocks (e.g., 1–10 mM). Acetonitrile may also be suitable for short-term handling.
• Aqueous media: Often limited solubility unless sulfonated; use 1–10% DMSO or DMF cosolvent, or add mild detergents (0.01–0.1% Tween‑20) or protein (e.g., BSA) to mitigate aggregation.
• pH effects: Neutral buffers (pH 6.5–8.0) generally preserve fluorescence and DBCO reactivity. Strongly basic solutions can accelerate bleaching/hydrolysis of the polymethine chain.

Polarity and miscibility (literature/general):

• Dye is amphiphilic with a hydrophobic DBCO; behaves as a moderately lipophilic cationic chromophore. Miscible in polar aprotic solvents; dispersibility in water depends on substituents (not specified here).

When to choose which solvent:

• Bioconjugation to azide-tagged biomolecules: Prepare a DMSO stock (e.g., 5–10 mM), then add to aqueous buffer to ≤10% DMSO final to maintain biomolecule integrity.
• Surface/particle labeling: Use DMF/DMSO for polymeric substrates, then exchange into aqueous buffer after quenching.

Quick comparison (general):

• DMSO: Highest solvating power; compatible with SPAAC. Potential to denature sensitive proteins if >10% v/v.
• DMF: Similar to DMSO; less viscous; ensure low amine content.
• Acetonitrile: Useful for analytical prep and quick dilutions; lower solubility for some cyanines.

Item-specific solubility values/logP/refractive index: Not specified for this item; refer to CoA/Spec Sheet.

Storage and Reconstitution

Item-specific storage/shipping (from Product Data):

• Storage conditions: Store at −20°C.
• Shipped in: Ice chest + ice pads.
• Research Use Note: For research use only.

General best practices for this class of dye:

• Light protection: Store in amber vials or wrap in aluminum foil. Minimize light exposure during handling.
• Atmosphere and moisture: Keep tightly sealed, desiccated, and preferably under inert gas (argon or nitrogen) to limit hydrolysis/oxidation of the polymethine chain.
• Reconstitution: Prepare stocks at 5–10 mM in anhydrous DMSO or DMF. Filter through a low-protein-binding 0.22 µm PTFE syringe filter if particulates are observed. Record the exact concentration spectrophotometrically if extinction coefficient is known (item-specific value not provided here).
• Aliquoting: Dispense single-use aliquots to avoid repeated freeze–thaw. Store solution aliquots at −20°C; for extended storage, consider −80°C. Avoid frost-free freezers with temperature cycling.
• Working solutions: Dilute into buffer immediately before use, keeping final DMSO/DMF ≤10% v/v to protect biomolecules. Avoid sodium azide in buffers during coupling.
• Stability/retention: Periodically check absorbance/emission to assess integrity. Discard if significant spectral shifts, precipitation, or reduced fluorescence are observed.

Any item-specific stabilizers, shelf life, or re-test dates: Not specified for this item; refer to CoA/Spec Sheet.

Structure and Identity

CY7 DBCO chloride is a near‑infrared (NIR) cyanine-7 fluorophore bearing a strained dibenzocyclooctyne (DBCO) moiety for copper‑free click conjugation; formulated as a chloride salt.

• SKU: C1449679
• Product name: CY7 DBCO chloride
• Intended use: For research use only (per Product Data)

Item-specific identifiers (from Product Data):

• CAS: Not specified for this item; refer to CoA/Spec Sheet.
• InChIKey: Not specified for this item; refer to CoA/Spec Sheet.
• SMILES: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

General structural description (literature/general knowledge):

• Core scaffold: Heptamethine cyanine (Cy7) chromophore consisting of two indolinium/benzindolium-type heteroaromatic rings bridged by a polymethine chain (7 methine units). Often exists as a cation balanced by a halide (here, chloride).
• Functionalization: A DBCO (dibenzocyclooctyne) group appended via an amide/urethane/alkyl linker (linker architecture varies by supplier) enables strain-promoted azide–alkyne cycloaddition (SPAAC) with azide-bearing targets.
• Ionic character: Typically a monocationic dye with Cl− as counterion; overall amphiphilic, with hydrophobic DBCO and cyanine core. Some Cy7 derivatives incorporate sulfonates for aqueous solubility; presence/absence here is not specified.
• Stereochemical features: The cyanine polymethine chain may adopt E/Z isomers; DBCO is a strained alkyne embedded in a bicyclic ring system that defines the reactivity toward azides.

2D structure in words (general): Two fused aromatic heterocycles connected by a linear conjugated chain (–CH=)×7, bearing N-alkyl substituents; a side chain terminates in a dibenzocyclooctyne ring; counterion is chloride.

Synthetic Utility

From a synthetic perspective, CY7 DBCO chloride is a functionalized reporter module combining:

• A reactive handle: DBCO strained alkyne for SPAAC with azides (bioorthogonal ligation) producing a 1,2,3‑triazole robust to hydrolysis and many biological conditions.
• A reporting unit: Cy7 heptamethine cyanine chromophore for NIR detection.

Utility in synthesis and materials:

• Modular installation of a NIR tag late in a synthesis by first introducing an azide (via, e.g., NHS–azide on lysines, alkyl/aryl azides, click-ready polymers), then coupling with DBCO–Cy7 under mild, metal-free conditions.
• Orthogonality: SPAAC is orthogonal to many common protecting groups and transformations, allowing parallel chemistries (e.g., thiol–maleimide, oxime ligation) on other handles.
• Surface modification: Immobilization on azide-presenting resins, silica, membranes, or nanoparticles to create fluorescent standards and sensors.
• Analytical tracking: The intense absorbance of cyanines enables facile quantitation of loading on solid supports or biomolecules through UV–Vis without radiolabels.

Considerations:

• Steric hindrance and local microenvironment can slow SPAAC; use linkers or adjust solvent composition to improve access.
• Cyanine stability: Protect from strong nucleophiles/bases that can attack the polymethine chain; avoid prolonged heating.
• Purification: Excess dye is readily removed from small biomolecules by RP-HPLC; for proteins, use SEC/desalting. Co-elution with hydrophobic products may require gradient optimization.

Item-specific reactivity modifiers, linker length, or substitution patterns: Not specified for this item; consult CoA.

Target Specificity

Not applicable. This product is a small-molecule fluorescent labeling reagent, not an antibody or affinity reagent. It has no inherent biological “target” specificity beyond the chemical selectivity of the DBCO–azide SPAAC reaction.

• Chemical selectivity (general): Reacts selectively with organic azides to form a triazole. Does not require metal catalysts. Avoid buffers containing sodium azide during the conjugation step to prevent depletion of reagent.