CY5-YNE - Moligand™, 10 mM in DMSO , CAS No.1345823-20-2

CAS: 1345823-20-2 Cat. No.: C1499684 PubChem CID: 132989613

GRADE & PURITY Moligand™, 10 mM in DMSO

Storage

Protected from light,Store at -80°C

Shipped In

Dry ice packs + Cold packs

Overview

CY5-YNE (Sulfo-Cyanine5-alkyne) is a reactive dye for the labeling of amino-groups in peptides , proteins, and oligonucleotides . CY5-YNE is a click chemistry reagent, it contains an Alkyne group and can undergo copper-catalyzed azide-alkyne cycloaddition (CuAAc) with molecules containing Azide groups.

Specifications

Specifications & Purity

Moligand™, 10 mM in DMSO

Storage

Protected from light,Store at -80°C

Shipped In

Dry ice packs + Cold packs

This product requires cold chain shipping. Ground and other economy services are not available.

Grade

Moligand™

Names and Identifiers

• PubChem CID: 132989613

Application Protocols

Example protocol 1: CuAAC labeling of an azide-modified peptide (general)

• Materials: azide-peptide (1 nmol), CY5-YNE (1.2–2.0 nmol), PBS pH 7.4, DMSO, CuSO4 (10 mM stock), sodium ascorbate (50 mM stock), THPTA ligand (10 mM stock), EDTA (0.5 M stock).
• Steps:
  1. Dissolve peptide in PBS (100 µL). Prepare CY5-YNE 10 mM stock in dry DMSO.
  2. Add CY5-YNE to 10–20 µM final (≤10% DMSO v/v).
  3. Add THPTA to 1 mM, then CuSO4 to 100 µM, then sodium ascorbate to 1 mM. Mix gently, protect from light.
  4. Incubate 30–60 min at room temperature.
  5. Quench with EDTA to 10 mM. Purify by spin desalting (G-25) or RP-HPLC as needed.
  6. Analyze by LC/MS and fluorescence.

Example protocol 2: Oligonucleotide labeling (general)

• Use 10–50 µM azide-oligo in HEPES (10 mM, pH 7.5) + 10% DMF. Add 2–3 eq CY5-YNE from DMSO stock. Add CuSO4 (100 µM), THPTA (1 mM), sodium ascorbate (1 mM). React 1–2 h, RT, dark. Quench with EDTA (10 mM). Desalt via ethanol precipitation or size-exclusion. Verify by MALDI/ESI-MS.

Notes and tips:

• Prepare copper/ascorbate fresh immediately before use.
• For proteins, maintain ≤10% organic co-solvent and consider 4–10°C if stability is a concern.
• Remove sodium azide from buffers prior to labeling.
• Degree of labeling can be estimated from A650/A280 with appropriate correction factors for the specific conjugate (determine empirically).

These are general/literature protocols; optimize for your specific substrate and application.

Biological Roles

CY5-YNE itself does not possess an intrinsic biological role; it functions as a fluorescent reporter when covalently attached to biomolecules.

General notes on Cy5 fluorophores in biochemical research (literature/context):

• Reporter function: provides far-red fluorescence with low autofluorescence background in biological samples; suitable for imaging, flow cytometry, and in-gel detection.
• Bioorthogonal labeling: via CuAAC to azide-labeled biomolecules produced by metabolic incorporation (e.g., azido sugars for glycan labeling) or site-specific chemical modification.
• Photophysics in biology: far-red excitation/emission reduces photodamage and scattering; signal quality can improve in protein-bound states due to reduced non-radiative decay.
• FRET/FLIM: Cy5 often serves as an acceptor in Cy3→Cy5 FRET pairs; spectroscopic properties depend on environment and linker length.

Caveats and best practices:

• Copper exposure during CuAAC can affect cell viability and protein function; for live systems, copper-free strategies are preferred.
• Protein labeling density influences brightness and function; optimize degree of labeling to balance signal and biomolecule activity.
• Avoid sodium azide in buffers during conjugation to prevent competition with azide-bearing targets.

Buffer Applications

This product is not a buffer reagent. However, buffer selection is critical for successful CuAAC labeling with CY5-YNE.

Practical buffer guidance (general):

• Compatible systems: PBS, HEPES, or phosphate buffers at pH 7.0–8.0 are commonly used. Avoid carbonate at high pH, which may accelerate dye degradation.
• Avoidants: remove sodium azide (NaN3) during conjugation—competes for copper and azide sites. Chelators (EDTA, EGTA) should be excluded during the reaction as they sequester Cu(I); they are useful after labeling to quench copper.
• Additives: include water-soluble Cu(I) ligands (e.g., THPTA at 0.5–2 mM) to protect biomolecules and accelerate the click reaction. 5–20% DMSO/DMF can aid dye solubility.
• Typical conditions (literature): pH 7.2–7.5, room temperature, 0.5–2 h; protein concentrations 10–100 µM; dye 1.1–5.0 equivalents relative to azide sites.
• Post-reaction: add EDTA (5–10 mM) to chelate copper, then purify by desalting spin columns or SEC.

Recipe hint (example, general):

• 1× PBS, pH 7.4; add THPTA to 1 mM; prepare fresh 10 mM CuSO4 and 50 mM sodium ascorbate stocks; mix to final 100–200 µM CuSO4 and 0.5–1.0 mM ascorbate immediately before adding to the reaction.

Green Alternatives

Sustainability considerations for Cy5 conjugation focus on minimizing copper usage, choosing benign solvents, and reducing energy/light exposure.

Comparison of options (general literature guidance):

• CY5-YNE (CuAAC) vs copper-free alternatives:

  • Advantages: fast kinetics with Cu(I), high selectivity, small reactive handle minimizes perturbation of biomolecules.
  • Trade-offs: requires copper salts and reducing agents; copper can damage sensitive biomolecules and demands careful waste handling.

• Alternative chemistries:

  • Cy5-DBCO or Cy5-BCN (SPAAC): avoids copper, enabling live-cell compatibility and simpler waste; trade-off is larger, more hydrophobic handle and sometimes slower kinetics/higher cost.
  • Tetrazine–TCO (iEDDA): bioorthogonal and very fast; however, handles can be bulkier and tetrazines can be less stable.

• Solvent and process greening:

  • Favor aqueous buffers with minimal DMSO/DMF co-solvent compatible with solubility.
  • Use water-soluble ligands (THPTA) to reduce copper loading (e.g., 50–200 µM Cu with ligand excess) while maintaining rate.
  • Implement micro-scale reactions to limit resource use; purify by desalting rather than extensive chromatography when possible.

Small comparison (qualitative):

• CuAAC (CY5-YNE): highest atom economy in bond formation; requires Cu/reductant; excellent selectivity.
• SPAAC (Cy5-DBCO): no metals, simpler workup; larger handle may affect biomolecule behavior; slower than optimized CuAAC.
• iEDDA (Cy5-tetrazine/TCO partner): fastest; no metals; potential stability concerns for tetrazine and higher synthetic cost.

Pharmaceutical Uses

This product is intended for research use only and is not an approved pharmaceutical excipient or active ingredient.

General context for cyanine dyes in pharmaceutical R&D (non-clinical, non-therapeutic):

• Process analytics and QC: fluorescent tracing in formulation/process development studies, e.g., tracking components in microfluidic mixing or filtration trials.
• Drug discovery tools: creation of fluorescent tracers for binding assays (fluorescence polarization, TR-FRET when paired appropriately), and target engagement measurements in biochemical assays.
• Device and material evaluation: labeling of polymers, nanoparticles, and medical device surfaces for in vitro imaging and characterization.

Notes:

• No pharmacopeial monograph is associated with CY5-YNE to our knowledge; item-specific regulatory status is Not specified for this item; refer to CoA/Spec Sheet.
• Any use in manufacturing or clinical settings requires independent qualification and compliance assessment by the user.

Physical Properties

Item-specific measured properties are not provided for this product. Refer to the CoA/Spec Sheet for definitive specifications.

Literature/general properties for Cy5-class alkynes (for context only):

• Appearance: typically dark blue to deep purple solid (literature, dye-class generalization).
• Spectral characteristics (Cy5 core, literature typical):
  • Absorption λmax: ~646–652 nm in aqueous/MeOH media (chromophore-dependent; substituents and medium affect exact value).
  • Emission λmax: ~662–670 nm.
  • Stokes shift: ~15–25 nm.
  • Extinction coefficient: often on the order of 200,000–270,000 M⁻1 cm⁻1 (varies with substitution and medium).
• Solubility (practical guidance):
  • High solubility in anhydrous DMSO and DMF (typical for cyanine dyes); water solubility depends strongly on sulfonation/ionic substituents (not specified for this item). Prepare concentrates in dry DMSO, then dilute into aqueous buffers with surfactant or co-solvent as needed.
• Partitioning: cyanine dyes are amphiphilic; precise logP/logD not specified for this item.
• Melting point, boiling point, density, refractive index, pKa: Not specified for this item; refer to CoA/Spec Sheet.

Notes:

• Photophysical properties are sensitive to environment (polarity, protein binding, aggregation). Validate λmax and quantum yield under your exact assay conditions.

Quality & Grades

• Grade/Purity: Moligand™ (item-specific). While a formal industry definition is not standardized for “Moligand™,” within research reagent contexts this designation typically indicates a high-quality, conjugation-ready small-molecule ligand/probe optimized for bioconjugation workflows.

What this typically implies (general guidance):

• Conjugation readiness: terminal alkyne functionality positioned to undergo efficient CuAAC with azide-bearing biomolecules (peptides, oligonucleotides, glycans, polymers, nanoparticles).
• Photochemical performance: Cy5-class dyes are selected for high brightness and good photostability relative to shorter-wavelength cyanines; batch-to-batch control is important for consistent brightness—consult the CoA for item-specific purity and spectral QC.
• Purity reporting: exact chemical purity (%), counterion identity, residual solvents/metals, and spectral acceptance criteria are Not specified for this item; refer to CoA/Spec Sheet.

Stabilizers/additives:

• No stabilizer information is provided for this item. If present, stabilizers or counterions will be disclosed in the CoA.

Recommended QC checks on receipt (user-side):

• Verify identity by absorbance/fluorescence spectra in the intended solvent.
• Check labeling efficiency in a small-scale CuAAC test reaction with an azide standard.
• Assess aggregation by recording spectra at multiple concentrations (look for peak broadening/shoulder formation).

Reaction & Applications

Primary role: CY5-YNE is designed for chemoselective labeling via copper-catalyzed azide–alkyne cycloaddition (CuAAC), enabling attachment of a Cy5 fluorophore to azide-bearing substrates.

• Core application areas:

  • Bioconjugation: labeling of azide-modified peptides, proteins (via azidohomoalanine, azido sugars, or azide-functional linkers), oligonucleotides, lipids, and polymers.
  • Materials and surfaces: immobilization on azide-functionalized nanoparticles, hydrogels, or self-assembled monolayers for imaging/sensing.
  • Assay development: creation of FRET pairs (with appropriate partners), fluorescence polarization tracers, and in-gel visualization tags.

• Chemistry notes (CuAAC):

  • Terminal alkyne undergoes 1,3-dipolar cycloaddition with organic azides in the presence of Cu(I), forming a 1,4-disubstituted 1,2,3-triazole with high regioselectivity.
  • Cu(I) is typically generated in situ from CuSO4 and sodium ascorbate; ligands such as TBTA or THPTA accelerate and protect biomolecules.
  • Reaction tolerates aqueous media, a broad pH window (~6–8), and diverse functional groups.

• Practical tips:

  • Use freshly prepared copper/ascorbate solutions; exclude air to limit dye/cargo oxidation.
  • Employ water-soluble Cu(I) ligands (THPTA) for protein/oligo labeling to reduce copper-induced damage.
  • For sensitive biomolecules, perform reactions at room temperature for 0.5–2 h; then quench copper with EDTA and purify by desalting or SEC.

• Not applicable/less typical:

  • Copper-free click (SPAAC) is not feasible with a simple terminal alkyne; use a strained alkyne (e.g., DBCO) if copper must be avoided.

Reaction Conditions

General, literature-based conditions for CuAAC labeling with terminal alkynes like CY5-YNE (optimize per system):

• Typical solvent/buffer: aqueous buffer (PBS or HEPES, pH 7.0–7.8) with 5–20% DMSO or DMF to maintain dye solubility.
• Catalyst system:
  • CuSO4·5H2O (50–200 µM final) + sodium ascorbate (0.5–2.0 mM) to generate Cu(I) in situ.
  • Ligand: THPTA or TBTA (0.5–2 mM) to stabilize Cu(I) and reduce biomolecule damage; THPTA is preferred for aqueous/biological systems.
• Stoichiometry: dye 1.1–5.0 eq relative to azide groups; for proteins with multiple azides, control degree of labeling by limiting dye equivalents.
• Temperature/time: room temperature, 30–120 minutes. For sensitive proteins, keep at 4–25°C and monitor.
• Atmosphere: ambient is acceptable; degassing can improve consistency. Prepare copper/ascorbate fresh to limit Cu(II) accumulation.
• Workup: quench with EDTA (5–10 mM), then desalting/SEC or ethanol precipitation (for oligonucleotides). Remove unreacted dye by spin columns or dialysis (MWCO selected to retain conjugate).
• Expected outcomes: near-quantitative conversion for small-molecule azides; 50–90% labeling efficiency for biomacromolecules depending on accessibility and conditions (literature ranges).

Notes:

• Avoid buffers containing azide or strong chelators during the reaction.
• Light-protect throughout to minimize photobleaching.
• Validate by absorbance/fluorescence ratio and mass spectrometry (for peptides/oligos).

Safety & Handling

GHS classification and hazard statements are not provided for this item. Always consult the product SDS for authoritative safety and regulatory information.

General laboratory safety guidance for cyanine fluorophores and alkynes (good practice):

• PPE: wear lab coat, nitrile gloves, and safety glasses. Handle powders and DMSO stocks in a fume hood to minimize inhalation/dermal exposure.
• Light sensitivity: the Cy5 chromophore is photolabile. Minimize light exposure (wrap containers with foil; use amber vials and subdued lighting).
• Storage incompatibilities: avoid strong oxidizers and strong acids/bases that can degrade the polymethine chain; avoid azides only in the context of preventing unintended click reactions in mixed stocks.
• Handling of DMSO solutions: DMSO enhances skin absorption; avoid contact. Use dedicated syringes or low-retention tips for accurate micro-volumes.
• Copper catalysis considerations (for CuAAC workflows): copper salts are harmful if swallowed/inhaled and can be acutely toxic to aquatic life—collect waste separately. Use appropriate chelators for decontamination (e.g., EDTA) before disposal per institutional policy.
• First aid overview (non-exhaustive; 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.
• Spills: cover solids with inert absorbent; avoid dust generation; collect in light-protected waste. For solutions, absorb with inert material and clean with detergent/water while minimizing light exposure.

Solvent Selection

Practical solvent choices for CY5-YNE focus on maintaining dye integrity, preventing aggregation, and enabling efficient conjugation.

• Polarity and miscibility (general for cyanine dyes):

  • Preferred stock solvents: anhydrous DMSO or DMF (high solvating power, miscible with water; minimize water to prevent hydrolysis of sensitive linkers if present).
  • Aqueous buffers: final conjugations commonly proceed in PBS, HEPES, or Tris-buffered saline with co-solvent (5–20% v/v DMSO/DMF) as needed for solubility.
  • Alcohols: MeOH/EtOH can solubilize many cyanines but may not be ideal for biomolecule integrity.

• When to choose which solvent:

  • DMSO: best for concentrated, long-term frozen stocks; low volatility and excellent dye solvation.
  • DMF: useful when DMSO is incompatible with a particular assay component; similar solvating ability.
  • Pure aqueous: only if the specific Cy5 derivative is sufficiently water-soluble (not specified for this item). Test at low concentrations to avoid aggregation.

• Practical tips:

  • Prepare a 5–20 mM stock in dry solvent under low light; filter (0.2 µm PTFE) if particulates are present.
  • Add stock slowly into vigorously mixed buffer to minimize local supersaturation/aggregation.
  • Avoid primary amine-rich buffers only if using amine-reactive chemistries; for this alkyne, amines are generally compatible. However, avoid buffers containing azide (NaN3) during conjugation to prevent competition.

• Comparison (general):

  • DMSO vs DMF: DMSO is less volatile and often preferred for long-term storage; DMF can be easier to remove under reduced pressure if required post-reaction.

Storage & Reconstitution

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

• Storage Conditions: Protected from light, Store at -80°C.
• Shipped In: Dry ice packs + Cold packs.

Reconstitution (general guidance):

• Allow the container to equilibrate to room temperature in the dark before opening to prevent moisture condensation.
• Prepare a concentrated stock solution (e.g., 5–20 mM) in anhydrous DMSO or DMF under low light. Vortex gently until fully dissolved.
• Optionally, filter the solution through a 0.2 µm PTFE syringe filter to remove particulates.

Aliquoting and stability (general):

• Aliquot stock solutions into amber, low-bind microtubes to avoid repeated freeze–thaw cycles.
• Store aliquots at -80°C, protected from light. Avoid frost-free freezers that warm during defrost cycles.
• Working solutions in aqueous buffer should be prepared fresh and used promptly; prolonged exposure to light and air may reduce fluorescence.

Handling notes:

• Minimize headspace oxygen and light during storage to limit oxidation/photobleaching of the cyanine core.
• Record preparation date and concentration on each aliquot; confirm concentration spectrophotometrically before critical experiments.

If any precipitation or color change is observed after storage, gently warm to room temperature and sonicate briefly; if unresolved, prepare a fresh solution. For definitive shelf-life and retest intervals, refer to the CoA/Spec Sheet.

Structure & Identity

Brief description: CY5-YNE is a Cy5-class heptamethine cyanine fluorophore bearing a terminal alkyne (–C≡CH) handle for copper-catalyzed azide–alkyne cycloaddition (CuAAC) bioconjugation.

• Product identifiers (item-specific):

  • SKU: C1499684
  • Product Name: CY5-YNE
  • CAS: 1345823-20-2
  • PubChem CID: 132989613
  • SMILES: Not specified for this item; refer to CoA/Spec Sheet.
  • InChIKey: 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.

• Structural features (general, literature description of Cy5-alkyne):

  • Core chromophore: heptamethine cyanine (Cy5-class) with two indolenine/benz[e]indolenine-type heteroaromatic end groups joined by a polymethine chain.
  • Functional handle: terminal alkyne (propargyl-like) for click chemistry.
  • Charge/state: Cy5 scaffolds are typically cationic or zwitterionic depending on substituents; precise ionization pattern for this item is not specified.
  • 2D structure in words: two nitrogen-containing fused aromatic systems connected by a seven-atom conjugated methine bridge; one terminus or side chain bears an –C≡CH group.
  • Stereochemistry: none expected on the terminal alkyne; E/Z isomerism along the polymethine can exist in cyanines, but specific isomer content is not specified for this item.

Synthetic Utility

From a synthetic chemistry perspective, CY5-YNE combines a far-red fluorophore with a terminal alkyne, enabling modular assembly of fluorescent constructs.

Key functional handle and reactivity:

• Terminal alkyne (–C≡CH):
  • CuAAC with organic azides → stable 1,4-triazole linkage (primary application).
  • Sonogashira coupling (literature) with aryl/vinyl halides under Pd/Cu catalysis is conceptually feasible but often impractical for sensitive dye scaffolds; if attempted, use mild conditions and protect the chromophore from light/oxidants.
  • Hydrothiolation/hydrosilylation (radical/metal-catalyzed) are possible in principle but rarely used with cyanines due to potential chromophore quenching.

Retrosynthetic value:

• The alkyne provides a convergent junction: complex azide-bearing ligands/biomolecules can be synthesized independently and joined at late stage.
• The triazole formed is chemically and enzymatically robust, offering stable linkages for downstream biological assays and materials applications.

Design considerations:

• Linker length/rigidity around the alkyne influences rotational freedom and can affect fluorescence (H-aggregation/quenching). Spacer design on the azide partner can mitigate aggregation-induced quenching.
• For multivalent constructs, iterative CuAAC provides a straightforward route to dendritic or polymeric Cy5 labeling.

Target Specificity

Not applicable for this product. CY5-YNE is a general-purpose fluorescent labeling reagent and does not have inherent biological target specificity (no antigen/epitope, clone, or isotype). Any specificity derives from the azide-bearing molecule to which it is conjugated.