Sulfo-Cyanine5 amine

Cat. No.: S171387

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Specifications

Condizioni di conservazione di stoccaggio

Store at -20°C

Spedito in

Ice chest + Ice pads

Questo prodotto richiede spedizione a catena fredda. I servizi di terra e altri servizi economici non sono disponibili.

Application Protocols

The following generalized procedures (literature) illustrate common uses of amine‑functional cyanine dyes. Adjust to your system; these are not item‑specific instructions.

• Stock solution preparation

  • Dissolve the dye at 1–10 mM in anhydrous DMSO or DMF. Vortex briefly, protect from light, and store aliquots at −20 °C.

• Conjugation to carboxylated biomolecules (EDC/sulfo‑NHS)

  1. Dissolve biomolecule (e.g., COOH‑PEG, carboxylated beads, peptide with C‑terminal COOH) in MES buffer (50 mM, pH 5.5).
  2. Add EDC (10–20 mM) and sulfo‑NHS (20–50 mM). Incubate 15–30 min at RT.
  3. Exchange buffer to phosphate (pH 7.4) if needed. Add dye stock to 1.5–3 eq per COOH; optionally add DIPEA (5–20 mM).
  4. React 1–2 h at RT protected from light. Quench with excess ethanolamine or Tris, then purify (spin column, SEC, or RP‑HPLC).

• Reductive amination to oxidized glycans

  1. Oxidize glycan residues on the target with NaIO4 (mild, on ice), desalt.
  2. Mix with dye (2–5 eq) in acetate buffer (pH 5.5) plus NaBH3CN (10–50 mM); incubate 2–4 h.
  3. Purify and characterize by UV‑Vis and fluorescence.

• Quality check

  • Record absorbance/emission spectra; determine dye‑to‑substance ratio using extinction coefficients (literature for Cy5‑type dyes). Confirm by LC‑MS where applicable.

Biological Roles

This product is a synthetic fluorescent label rather than a native metabolite.

• Functional role (general/literature)

  • Acts as a near‑IR reporter (Cy5 class) for detection and quantitation in biochemical assays, imaging, and separation techniques. The sulfonate groups reduce nonspecific interactions with proteins and membranes, improving aqueous performance.

• Biochemical utility (research context)

  • Conjugation to biomolecules enables tracking of proteins, peptides, oligonucleotides, glycoconjugates, and nanoparticles in vitro. The amine handle allows coupling to activated carboxyls and aldehydes (after oxidation of carbohydrates), supporting site‑selective labeling strategies.
  • Excitation/emission in the red region minimizes autofluorescence from biological matrices and is compatible with many standard laser lines (e.g., 633–647 nm excitation; literature).

• Photochemical considerations (literature)

  • Subject to photobleaching and potential singlet oxygen generation upon intense illumination; use deoxygenated buffers or antifade systems for sensitive measurements.

No clinical or therapeutic roles are implied. All uses are for research and laboratory investigations only, as stated in the product data.

Buffer Applications

This material is not a buffering reagent. However, buffer choice is critical for successful bioconjugation with an amine‑functional dye:

• General guidance (literature)
  • EDC/sulfo‑NHS activation of carboxyls: Use MES (25–100 mM, pH 5.0–6.0) for activation, then couple with the dye amine in phosphate or borate buffer (pH 7.2–8.5) while balancing amine deprotonation and biomolecule stability.
  • Reductive amination: Perform Schiff‑base formation in acetate or phosphate buffer (pH 5.5–6.5), followed by mild reducing agent (e.g., sodium cyanoborohydride or picoline borane) in the same buffer.
  • Avoid primary amine‑containing buffers (e.g., Tris, glycine) during coupling, as they compete with the intended reaction.

These are general, literature‑based practices and not item‑specific specifications.

Green Alternatives

• Solvent and process choices (greener practice, literature/general)

  • Favor aqueous buffers with minimal DMSO/DMF cosolvent when performing EDC/sulfo‑NHS couplings; use MES or phosphate buffers to reduce organic solvent usage.
  • Where organic solvent is required, consider ethanol or 2‑MeTHF for compatible steps (e.g., workups), acknowledging the dye’s ionic nature may limit solubility.
  • Employ micro‑scale reactions and high‑recovery purification (e.g., semi‑prep RP‑HPLC, solid‑phase capture/release) to minimize waste.

• Comparison of solvent options (general)

  • DMSO: excellent solubilizer; higher boiling point complicates removal; relatively low toxicity vs DMF.
  • DMF: strong solvency but reproductive toxin; replace with DMSO or aqueous media when feasible.
  • Aqueous buffers: preferred for EDC/sulfo‑NHS; avoid excessive halogenated solvents in workup.

• Photostability and waste reduction

  • Use anti‑fade reagents and oxygen scavengers in applications to prolong signal and reduce repeat experiments.
  • Collect dye‑containing aqueous/organic wastes separately for proper disposal; cyanine dyes are strongly colored and trace‑detectable.

Note: The chemistry and ionic character of sulfonated cyanines inherently favor water as a greener reaction medium for many conjugations.

Pharmaceutical Uses

• This product is not an active pharmaceutical ingredient. No therapeutic or clinical claims are made.

• Potential roles in pharmaceutical R&D (non‑clinical, general)

  • Analytical tracer in formulation studies to visualize distribution of carriers (e.g., liposomes, polymer conjugates) in in vitro models.
  • Fluorescent tag for process development, impurity tracking, and stability studies of bioconjugates.
  • Tool compound for method qualification in CE/HPLC with fluorescence detection.

• Excipient status and compendia

  • No pharmacopeial monograph is implied for Sulfo‑Cyanine5 amine. Any use in regulated settings should be supported by internal qualification, vendor CoA, and relevant validation data.

All uses are limited to laboratory research and development. Consult quality/regulatory teams before any use in manufacturing or clinical contexts.

Physical Properties

• Item-specific properties

  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
  • Refractive index / density / melting point / boiling point: Not specified for this item; refer to CoA/Spec Sheet.
  • Solubility (spec): Not specified for this item; refer to CoA/Spec Sheet.

• Optical properties (literature, for the Cy5 class; actual values can vary with solvent, pH, and substitution)

  • Absorption maximum (λmax): typically ~640–650 nm (literature for Cy5‑type dyes).
  • Emission maximum (λem): typically ~660–670 nm (literature).
  • Molar extinction coefficient: often in the 200,000–250,000 M−1·cm−1 range (literature, dye‑dependent).
  • Quantum yield: variable; commonly 0.2–0.35 in aqueous buffers for sulfonated Cy5 analogs (literature, formulation‑dependent).

• Solubility and polarity (literature/general)

  • Sulfonate groups confer high aqueous solubility; the dye also dissolves in polar aprotic solvents (DMSO, DMF) used for stock solutions.
  • The primary amine may be protonated (reduced nucleophilicity) below pH ~7–8; deprotonated form is favored at higher pH.

• Photophysical notes (literature)

  • Strongly fluorescent; subject to photobleaching under intense illumination—use antifade agents and minimize light exposure.

All quantitative values above are literature/general for Cy5‑type dyes and are not specifications for this item.

Quality and Grades

• Item-specific grade/purity: Not specified for this item; refer to CoA/Spec Sheet.

• Interpreting common grades for fluorescent dyes (general guidance)

  • “Dye content” or “purity by HPLC” typically reflects the proportion of the principal chromophore relative to side products and homologs; higher values are critical for reproducible labeling and photophysics.
  • “Desalting” or “counterion specification” (e.g., triethylammonium, sodium) can impact solubility and mass spectrometry readout.
  • “Isomeric composition” may be noted for cyanines; consistent isomer ratios improve lot‑to‑lot consistency in brightness and mobility in electrophoresis/HPLC.

• Stabilizer considerations (general)

  • Some dye solids are supplied with trace stabilizers or as mixtures with salts to enhance handling; absence/presence should be disclosed on the CoA/SDS.

• Recommended QC on receipt (practical tips)

  • Verify identity by LC‑MS (expected parent ion for Cy5‑sulfo‑amine class), purity by analytical HPLC at 650 nm detection, and fluorescence spectrum in PBS vs. methanol to confirm expected λmax/λem (literature values for Cy5‑type dyes).
  • Run a small‑scale test conjugation to a model activated carboxyl (e.g., NHS‑activated PEG) to assess coupling efficiency and background.

Reaction and Applications

• Core application (general for amine‑functional cyanine dyes)

  • Fluorescent labeling via formation of amide, urea/carbamate, or sulfonamide linkages. The primary amine acts as a nucleophile toward appropriately activated electrophiles.

• Common conjugation strategies (literature)

  • EDC/NHS coupling: Activate carboxyl groups on polymers, peptides, oligonucleotides, or beads with EDC/NHS (or sulfo‑NHS), then couple with Sulfo‑Cyanine5 amine to form stable amide bonds in mildly basic buffers.
  • Isothiocyanate or NHS‑carbonate route (two‑step synthesis): Convert the amine dye to an isothiocyanate or NHS‑carbonate intermediate for later labeling of amines or alcohols.
  • Reductive amination: Condense the dye amine with aldehydes (e.g., oxidized glycans) followed by NaBH3CN or picoline borane reduction to form secondary amines.
  • Acyl chloride/activated ester reactions: Direct coupling to acyl chlorides or activated esters on small molecules to build custom probes.

• Use cases

  • Preparation of reference standards and spike‑in controls for NGS, flow cytometry, in‑gel fluorescence, and fluorescence plate assays (non‑clinical research).
  • Site‑specific labeling of carboxylated nanoparticles, self‑assembled monolayers (COOH‑SAMs), or PEG spacers for imaging and tracking experiments.

• Practical tips

  • Maintain dye in low‑water solvents for stock; avoid prolonged exposure to base or light. Use slight excess of dye or electrophile to drive coupling; purify by RP‑HPLC (monitor at ~650 nm). Include 0.01–0.05% base (DIPEA) when needed to keep the amine nucleophilic.

Reaction Conditions

The following are literature‑based, general conditions for amine‑bearing cyanine dyes; optimize for your substrate and avoid harsh conditions that may damage the polymethine chromophore.

• Amide formation via EDC/sulfo‑NHS (carboxyl on substrate)

  • Activation: 1–10 mM substrate COOH in MES buffer (pH 5.0–6.0), 5–20 mM EDC, 5–50 mM sulfo‑NHS, 15–30 min at RT.
  • Coupling: Adjust to pH 7.2–8.0 (phosphate or borate), add 1.2–3.0 eq Sulfo‑Cyanine5 amine, react 1–2 h at RT (or 4 °C overnight for sensitive biomolecules).

• Reductive amination (aldehyde on substrate)

  • 50–100 mM acetate or phosphate buffer, pH 5.5–6.5; 1.5–5 eq dye; 10–50 mM NaBH3CN or picoline borane; 1–4 h at RT. Quench and purify by desalting/HPLC.

• Carbamate/urea formation

  • In anhydrous DMF or DMSO, activate alcohol/amine‑bearing linker with DSC or triphosgene derivative, then couple with the dye amine in presence of DIPEA or TEA (2–5 eq) at 0–25 °C, 1–3 h.

• Purification and analysis

  • RP‑HPLC (C18) with water/ACN + 0.1% TFA or formic acid; monitor 640–670 nm. Typical recoveries depend on substrate; yields vary widely (30–90%).

All parameters above are general literature guidance and are not specifications for this item.

Safety and Handling

• Regulatory/SDS

  • GHS classification: Not specified for this item; refer to SDS.
  • Signal word / H‑statements / pictograms: Not specified for this item; refer to SDS.
  • Research use: For research use only (as stated in product data).

• General laboratory precautions (good practice; not a substitute for SDS)

  • Wear appropriate PPE: lab coat, gloves (nitrile), safety glasses.
  • Handle as a light‑sensitive dye; protect from light to avoid degradation.
  • Avoid inhalation of dust/aerosols and contact with skin/eyes. Work in a well‑ventilated area or fume hood during weighing/dissolution.

• Incompatibilities and stability (general)

  • Avoid strong oxidizers and strong acids/bases that may degrade the polymethine chain or amine functionality.
  • Aqueous solutions are susceptible to hydrolysis/oxidation over time; prepare fresh or store aliquots at low temperature protected from light and air.

• First‑aid overview (general)

  • Skin/eye contact: Rinse with plenty of water for at least 15 minutes; remove contaminated clothing. Seek medical attention if irritation persists.
  • Ingestion/inhalation: Move to fresh air, rinse mouth, and seek medical advice.

Always consult the product’s SDS for authoritative hazard, exposure limits, and emergency procedures.

Solvent Selection

• Polarity and solubility profile (literature/general for sulfonated Cy5 dyes)

  • Highly water‑soluble due to sulfonate substituents; also soluble in polar aprotic solvents such as DMSO and DMF, which are commonly used for concentrated stock solutions (e.g., 1–10 mM).
  • Limited solubility in nonpolar solvents (e.g., hexanes, toluene) due to ionic character.

• Practical solvent choices by use case

  • Bioconjugation to activated carboxyls (EDC/NHS strategy): aqueous buffers (MES pH 5.5–6.0 or phosphate pH 7.2–7.6) with 0–30% DMF or DMSO cosolvent for solubility.
  • Urea/carbamate formation with activated carbonates: anhydrous DMF, DMSO, or acetonitrile under inert atmosphere.
  • Analytical characterization: MeOH/H2O or ACN/H2O with 0.1% TFA or formic acid for LC‑MS.

• Comparison to alternatives (general)

  • Versus non‑sulfonated Cy5 amine: sulfo analogue shows superior aqueous solubility and lower nonspecific binding but can be more challenging to extract into organic phases.
  • Versus NHS‑ester dyes: amine dyes require a carboxyl‑activation step on the biomolecule or scaffold; NHS esters directly label amines but are moisture‑sensitive.

• Tips

  • Filter or centrifuge dye stocks to remove particulates; protect from light. Adjust pH to ensure the amine is in its reactive, deprotonated state when nucleophilicity is required.

Storage and Reconstitution

• Item-specific storage and shipping

  • Storage conditions: Store at −20 °C (per product data). Protect tightly from light and moisture.
  • Shipped in: Ice chest + ice pads (per product data).

• Reconstitution (general guidance)

  • Prepare concentrated stocks (e.g., 1–10 mM) in anhydrous DMSO or DMF. For immediate aqueous use, dilute into buffer just before the experiment. If high aqueous solubility permits, small volumes of water or PBS may also be used.
  • Filter or centrifuge stock to remove any particulates before use.

• Handling and aliquoting

  • Store aliquots to avoid repeated freeze–thaw cycles. Use amber vials or wrap containers in foil to minimize light exposure.
  • Avoid prolonged exposure to elevated temperatures or basic pH, which can degrade the polymethine chain.

• Shelf life and stability

  • Solid and frozen DMSO stocks are generally stable for months when protected from light and air; however, exact stability and expiry are Not specified for this item; refer to CoA/Spec Sheet.

Always equilibrate cold vials to room temperature in the dark before opening to prevent condensation.

Structure and Identity

Sulfo-Cyanine5 amine is a water-soluble, near‑infrared cyanine fluorophore bearing a primary amine handle for conjugation chemistry.

• Item-specific identifiers

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

• Structural features (general/literature description, not item-specific)

  • Core scaffold: a polymethine (heptamethine-like) cyanine chromophore bridging two indolenine/benz[e]indolenine heteroaromatic rings.
  • Functional groups: multiple sulfonate substituents (to impart high aqueous solubility) and a terminal primary amine (-NH2) used as a nucleophile for coupling.
  • Charge state: typically zwitterionic or net anionic in water due to sulfonates; protonation state of the amine depends on pH.
  • Conjugation: extended π‑system responsible for strong absorption in the red/near‑IR region (Cy5 class).

• 2D structure in words (literature)

  • Two nitrogen-containing aromatic systems at each end, linked by a conjugated polymethine chain; sulfonate groups pendant on the aromatic rings, and one ring or side chain bearing a primary aliphatic amine suitable for amide, urea, or sulfonamide formation.

Note: Exact substitution pattern, counterions, and stereodescriptors (if any) are not specified for this catalog item.

Synthetic Utility

• Functional group leverage

  • Primary amine enables formation of amide (with activated carboxyls), urea/carbamate (with activated carbonates/chloroformates), and sulfonamide (with sulfonyl chlorides) linkages, anchoring the dye to diverse scaffolds.

• Retrosynthetic perspective (general)

  • The dye can be viewed as a nucleophilic module appended to a Cy5 chromophore; many probe architectures arise by coupling to electrophile‑bearing linkers (PEGs, click‑handles, affinity ligands), enabling modular probe synthesis.

• Named/standard transformations (literature)

  • EDC/sulfo‑NHS amide coupling in aqueous media for bioconjugates.
  • DSC/CBT carbonate activation to generate carbamates linking to alcohol‑bearing substrates.
  • Reductive amination onto aldehyde‑decorated glycoconjugates or polymers.
  • SuFEx‑type or sulfonyl chloride chemistry to yield robust sulfonamides (where compatible with the chromophore).

• Practical notes

  • Maintain mild temperatures and neutral to slightly basic pH to preserve the polymethine chain. Use minimal light and oxygen. For hydrophobic targets, introduce hydrophilic linkers to maintain solubility and reduce aggregation.
  • Purify by RP‑HPLC with detection at ~650 nm; confirm structure by HR‑MS and, if needed, 1H NMR in D2O or DMSO‑d6 with light protection.

Target Specificity

Not applicable. This product is a small‑molecule fluorescent dye, not an antibody or affinity reagent with defined biological target specificity. Any selectivity arises from the conjugated ligand or biomolecule to which the dye is attached.