DBCO-NHCO-PEG2-CH2COOH , CAS No.D1445666

CAS: D1445666 Cat. No.: D1445666 Formule: C₂₆H₂₈N₂O₆ Poids moléculaire: 464.51

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Vue d’ensemble

DBCO-NHCO-PEG2-CH2COOH is a PEG-based PROTAC linker that can be used in the synthesis of PROTACs. DBCO-NHCO-PEG2-CH2COOH is a click chemistry reagent, it contains a DBCO group that can undergo strain-promoted alkyne-azide cycloaddition (SPAAC) with molecules containing Azide groups.

Specifications

Conditions de stockage de stockage

Store at -20°C

Expédié en

Ice chest + Ice pads

Ce produit nécessite l'expédition en chaîne froide. Les services terrestres et autres services économiques ne sont pas disponibles.

Noms et identifiants

Poids moléculaire

464.51

Application Protocols

No tested application protocols, methods, or recommended dilutions are specified for this item. Refer to the literature and your internal SOPs for SPAAC labeling or EDC/NHS coupling workflows appropriate to your system.

For planning purposes only: Select buffers and stoichiometries that match your substrate (protein, peptide, surface, polymer), and validate conditions (time, temperature, equivalents) at small scale before scale-up.

Biological Roles

This compound is a synthetic bioconjugation reagent and has no known endogenous biological role.

General/literature perspective:

• Bioorthogonal handle: The DBCO moiety reacts selectively with azides without interacting significantly with native biological functional groups, enabling labeling in complex matrices and live-cell contexts when properly formulated.
• PEG spacer effects: The short PEG2 linker reduces hydrophobic interactions relative to bare aromatic alkynes and can modestly improve aqueous compatibility. PEG spacing also distances the DBCO reactive center from the substrate, minimizing steric hindrance in biomolecular reactions.
• Non-specific interactions: While PEG mitigates nonspecific binding, the aromatic DBCO core can still contribute to hydrophobic interactions; optimizing linker length or incorporating charged groups can further tune behavior for specific biological environments.

Important note: All uses are limited to research applications. This product is not intended for diagnostic, clinical, or therapeutic use.

Buffer Applications

This reagent is not a buffer component; however, buffer choice is important for its intended coupling and click reactions.

General/literature guidance:

• SPAAC labeling: Perform in neutral buffers such as PBS or HEPES, pH ~6.8–7.8. Include minimal organic cosolvent (e.g., 2–10% DMSO) if needed for solubility. Avoid primary amine-containing buffers (e.g., Tris) only when you are conducting carboxyl activation steps; for SPAAC alone, Tris is usually acceptable.
• EDC/NHS coupling of the –COOH: Use amine-free, mildly acidic buffers like MES (pH ~5.0–6.0) for activation; subsequently adjust to pH ~7–8 when reacting with the amine target to form the amide. Maintain ionic strength compatible with your biomolecule.
• Desalting and cleanup: After labeling, remove excess small molecules by gel filtration (e.g., size-exclusion spin columns) or dialysis into your target buffer.

These are general conditions from literature practice; optimize empirically for your specific system.

Green Alternatives

DBCO-mediated SPAAC is inherently “greener” than CuAAC in contexts where copper catalysts and reducing agents are undesirable or generate metal-containing waste. Additional green chemistry choices focus on solvent systems and reagent selection.

Greener choices (general/literature):

• Metal-free bioorthogonal click: SPAAC with DBCO avoids Cu(I) catalysts (and auxiliary ligands/reductants), reducing toxicity and waste treatment burden relative to CuAAC.
• Solvent selection: Favor water-rich buffers with minimal cosolvent (≤10% DMSO or ethanol) for bioconjugations. For synthetic steps, consider 2‑MeTHF or CPME in place of chlorinated solvents when polarity and stability allow.
• Atom economy: SPAAC forms a single triazole product without auxiliary byproducts; EDC-mediated amide formation produces urea byproducts—alternatives like CDI (in appropriate contexts) may reduce aqueous waste streams.

Comparison snapshot (contextual):

• SPAAC (DBCO + azide): No metal, ambient temperature, aqueous-compatible; tradeoff is sometimes slower kinetics than CuAAC at very low concentrations.
• CuAAC (terminal alkyne + azide + Cu): Fast and high yielding but requires copper sources, reductants (e.g., ascorbate), and ligand systems; extensive cleanup may be needed for biological use.
• BCN or DIBAC analogs: Similar metal-free performance; some variants offer improved hydrophilicity or different kinetics. Selection can be based on solubility or stability in your matrix.

Note: Always balance green metrics with performance, stability of strained alkynes, and the integrity of sensitive biomolecules.

Pharmaceutical Uses

No pharmacopeial status or excipient role is specified for this item.

General/process-development context:

• Linker installation: DBCO‑PEG‑carboxyl reagents are used in research and process development to install a SPAAC‑competent handle onto amine-bearing intermediates (peptides, proteins, polymers, nanoparticles) prior to metal-free conjugation with azide-functional payloads.
• Manufacturing considerations: The copper-free nature of the subsequent click step can simplify impurity profiles by avoiding residual metals. PEG2 provides compact spacing; longer PEGs may be selected to tune hydrophilicity and ADC/protein conjugate properties in development settings.
• Regulatory note: Any use in cGMP or clinical manufacturing would require thorough qualification of identity, purity, residual solvents, and impurity profiles from lot-specific documentation. This listing is for research use only and is not approved for therapeutic or diagnostic applications.

Physical Properties

Item-specific physico-chemical specifications are not supplied for this product.

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Purity/grade: 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.
• Melting/boiling point: Not specified for this item; refer to CoA/Spec Sheet.
• Density, refractive index: Not specified for this item; refer to CoA/Spec Sheet.

General/literature expectations for DBCO–PEG–COOH analogs (for context only; not item specifications):

• State: Typically solid to semi-solid depending on PEG length and substituents.
• Solubility: Good in polar aprotic solvents (DMSO, DMF, acetonitrile); often soluble in alcohols. Aqueous solubility improves with PEG content and salt formation; PEG2 variants may require co-solvent.
• Ionization: Terminal –COOH with typical carboxyl pKa ~4–5 (literature), enabling formation of sodium/potassium salts for enhanced water solubility.
• LogP/logD: Moderated by DBCO’s aromaticity and PEG’s polarity; overall amphiphilic behavior.

Note: For experimental parameters relevant to your application (e.g., water content, residual solvents, UV cutoff), consult the product’s Certificate of Analysis (CoA) or Specification Sheet.

Quality and Grades

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

Guidance for interpreting grades (general):

• Research grade bioconjugation reagents are typically provided at high chemical purity suitable for synthetic and labeling work. Analytical controls may include NMR, HPLC/UPLC purity, and HRMS.
• For click-ready strained alkynes (DBCO), trace metal and water content can influence downstream performance only indirectly (e.g., in EDC/NHS activation efficiency of the –COOH). Where low UV background is required (analytical monitoring), HPLC-grade solvents are recommended but are not a property of this solid reagent.
• Stabilizers: None are indicated. If stabilizers or inhibitors are present for a given lot, this will appear on the CoA or Spec Sheet.
• Item-specific assurances (storage/shipping): This item ships cold (ice chest + ice pads) and should be stored at −20°C, supporting shelf-life and integrity of the strained alkyne and activated intermediates you may generate.

Recommendation: For regulated workflows, request and review the lot-specific CoA/Spec Sheet for exact purity, identification methods, residual solvents, and any additional quality attributes.

Reaction and Applications

Primary utility (general/literature):

• Copper-free click chemistry: The DBCO core undergoes rapid strain-promoted azide–alkyne cycloaddition (SPAAC) with organic and biomolecular azides, forming stable 1,2,3‑triazoles without copper catalysts. Useful for live-cell compatible labeling, polymer modification, and surface functionalization where metal avoidance is critical.
• Conjugation handle: The terminal –CH2COOH enables straightforward amide bond formation to primary amines (e.g., lysine residues on proteins/peptides, amine-terminated surfaces) via EDC/HOBt or EDC/NHS activation, installing a DBCO tag for subsequent SPAAC.

Typical workflows:

1. Install DBCO: Activate the –COOH (EDC/NHS) in mildly acidic buffer (MES, pH ~5–6) or anhydrous DMF with base; react with amine-bearing target to yield a DBCO-functional conjugate.
2. Click with azide: Expose the DBCO-modified target to an azide partner (fluorophore, biotin, drug, surface) in PBS/HEPES (pH 6.8–7.8) at ambient temperature; reaction typically reaches completion in minutes to a few hours depending on concentrations.

Practical considerations:

• PEG2 length offers compact spacing; for bulky targets or to mitigate steric hindrance, consider longer PEGs.
• Maintain azide/DBCO stoichiometry at ≥1.2:1 to drive SPAAC to completion on dilute biomolecule systems; remove excess by desalting or dialysis.
• Avoid high concentrations of competing nucleophiles during carboxyl activation to limit hydrolysis; conduct couplings swiftly under dry conditions.
• DBCO is generally stable to common buffers and physiological pH; protect from strong UV and heat over extended periods.

Reaction Conditions

Guidance below reflects general literature practices; adjust to your system. No item-specific specifications are provided.

SPAAC (DBCO + azide):

• Solvent/buffer: PBS or HEPES, pH 6.8–7.8; 0–10% DMSO to aid solubility as needed.
• Concentrations: For biomolecule labeling, 5–100 µM limiting partner is common; use 1.2–5.0 molar equivalents of the azide or DBCO counterpart to drive completion.
• Temperature/time: Ambient (20–25°C), typically 15 min to several hours depending on dilution and sterics; gentle agitation improves mass transfer.
• Notes: Remove excess small-molecule partner by desalting or dialysis; monitor by UV–Vis/HPLC/MS as appropriate.

Amide coupling via –COOH (installation of DBCO onto amines):

• Activation: EDC (with NHS or sulfo‑NHS) in MES buffer (pH ~5–6) or EDC/HOBt in anhydrous DMF. Minimize water and perform at 0–25°C to reduce O‑acylisourea hydrolysis.
• Coupling: Adjust to pH ~7.5–8.5 for amine addition in aqueous systems, or add base (e.g., DIPEA) in organic media. Typical reaction times 0.5–4 h.
• Quenching/purification: Scavenge excess reagents; purify by SEC for proteins or flash/preparative HPLC for small molecules.

Stability considerations:

• Protect from strong light/heat over extended periods. DBCO is generally stable under neutral conditions but avoid strong bases and high temperatures that can compromise strained ring integrity.

Safety and Handling

Item-specific hazard classification and GHS details are not provided for this listing. Always consult the SDS for authoritative information.

• GHS classification, signal word, pictograms, H‑statements: Not specified for this item; refer to SDS.
• Likely hazards (general for DBCO–PEG–COOH analogs): May cause skin/eye irritation. Avoid inhalation of dust/particulates and direct contact. DBCO is a strained alkyne that reacts selectively with azides; it is otherwise reasonably stable under ambient laboratory conditions.
• PPE: Use lab coat, safety glasses, and appropriate chemically resistant gloves. Handle in a fume hood when weighing or preparing solutions.
• Incompatibilities (general): Strong oxidizers; strong bases/acids that could hydrolyze the amide or ester impurities; azide-containing reagents if unintended SPAAC is not desired. Avoid reactive acylation agents near the free acid unless coupling is intended.
• Handling tips: Use dry, oxygen- and moisture-minimized technique for coupling steps (EDC/NHS) to maintain anhydrous conditions. Protect from prolonged light and heat to minimize degradation of strained alkyne motifs.
• First aid overview: In case of contact, rinse with water for at least 15 minutes; remove contaminated clothing. If inhaled, move to fresh air. If ingested or in case of exposure symptoms, seek medical advice. Refer to SDS.
• Waste: Collect organic solutions and aqueous workups containing coupling byproducts as chemical waste; dispose per institutional and local regulations.

Solvent Selection

DBCO-NHCO-PEG2-CH2COOH is amphiphilic: an aromatic DBCO core joined to a short PEG spacer and a terminal carboxylic acid. Solvent choice depends on whether you are performing (a) SPAAC labeling with azides or (b) amide coupling via the –COOH group.

General/literature guidance:

• Polar aprotic solvents: DMSO and DMF dissolve DBCO–PEG–COOH efficiently and are common stock-solution vehicles (10–50 mM) for subsequent dilution into aqueous buffers.
• Aqueous buffers: Direct dissolution may be limited for PEG2; cosolvents (2–20% DMSO, DMF, or ethanol) enable homogeneous SPAAC with biomolecules. Forming sodium/potassium salts of the carboxylate can increase water solubility.
• Alcohols: Methanol, ethanol, isopropanol can be used for small-molecule synthesis steps, extractions, and rinses.
• Nonpolar solvents: Acetonitrile and ethyl acetate are often suitable for chromatography and workup; toluene/MTBE may be used depending on polarity of intermediates.

When to choose alternatives:

• For highly aqueous bioconjugations, longer spacers (e.g., PEG4/PEG8) or zwitterionic linkers provide improved solubility and reduced aggregation.
• For strictly aqueous, metal-free labeling, BCN- or DBCO-sulfo derivatives can be more hydrophilic.

Small comparison (general):

• DMSO: maximal solubilization; miscible with water; compatible with SPAAC after dilution.
• DMF: strong solvent for coupling setups; minimize exposure in biological systems.
• Buffer (MES/HEPES/PBS) + 5–10% DMSO: balances solubility with biomolecule integrity for SPAAC.

Storage and Reconstitution

Item-specific conditions:

• Storage: Store at −20°C.
• Shipping: Shipped in ice chest with ice pads.
• Research Use: For research use only.

General guidance (literature/practice; not product specifications):

• Protect from moisture and light; keep container tightly closed under inert atmosphere or with desiccant when feasible.
• Allow vial to warm to room temperature before opening to prevent condensation.
• Reconstitution: Prepare concentrated stocks in anhydrous DMSO or DMF (e.g., 10–50 mM). Filter if particulates are present. For aqueous use, dilute immediately into buffer (e.g., PBS/HEPES) to the desired working concentration, optionally with 2–10% cosolvent.
• Aliquoting: Divide stock into single‑use aliquots and store at −20°C to minimize freeze–thaw cycles. Avoid repeated thawing; discard aliquots showing precipitation or degradation.
• Stability: Monitor by LC/MS or HPLC for long-term projects. Avoid prolonged exposure to strong bases or elevated temperatures that may compromise the strained alkyne or linkage integrity.

Structure and Identity

Item-specific identifiers provided: SKU D1445666; Product Name DBCO-NHCO-PEG2-CH2COOH. Other identifiers are not supplied for this listing.

• 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: D1445666 (catalog reference; CAS number not specified).

Structural description (general/literature):

• Core scaffold: DBCO (dibenzocyclooctyne), a strained cyclooctyne fused to two benzene rings enabling copper-free azide–alkyne cycloaddition (SPAAC).
• Linkage: “NHCO” indicates an amide/urea-type linkage from the DBCO side to a short polyethylene glycol spacer.
• Spacer: PEG2 (two ethylene glycol units) provides hydrophilicity and spacing to reduce steric hindrance during bioconjugation.
• Terminus: CH2COOH denotes a terminal methylene carboxylic acid handle for carbodiimide-mediated coupling to primary amines (e.g., lysines on proteins) or for further derivatization (e.g., NHS ester formation).
• Stereochemistry: No defined stereocenters are expected in the PEG/DBCO construct; the ring strain in DBCO drives reactivity rather than stereochemistry.

2D depiction in words: Two benzene rings share a fused junction with an eight‑membered alkyne-containing ring (cyclooctyne). From one aromatic/bridge position, an amide (–NH–C(=O)–) links to –CH2–CH2–O–CH2–CH2–O–CH2–COOH, ending with a carboxylic acid.

Synthetic Utility

Functional group portfolio (general/literature):

• Strained alkyne (DBCO): Highly selective toward organic/biological azides via SPAAC, forming triazoles under mild, metal-free conditions.
• Carboxylic acid terminus: Amenable to carbodiimide-mediated amide coupling to primary amines; convertible to activated esters (e.g., NHS, PFP) or to acid chlorides under strictly controlled conditions.
• PEG2 spacer: Enhances solubility in polar media and provides spatial separation between the reactive alkyne and the conjugation site for better accessibility.

Representative transformations:

• Amide formation: EDC/HOBt or EDC/NHS in DMF or MES buffer yields DBCO‑PEG2 amides on peptides, proteins, or surfaces.
• Esterification: DCC/DMAP with alcohol partners to install cleavable or protecting groups.
• SPAAC ligations: Rapid coupling to azido‑fluorophores, azido‑biotin, azido‑polymers, or azido‑surfaces to afford stable triazole‑linked conjugates.

Retrosynthetic value:

• As a modular intermediate, DBCO‑PEG2‑COOH can be integrated late‑stage into complex molecules, decoupling the SPAAC handle installation from upstream synthesis. The carboxyl allows convergent assembly with diverse amine-bearing scaffolds.

Practical notes:

• Keep carboxyl activation steps anhydrous and brief to limit hydrolysis. For biomolecules, use amine-free buffers and immediately introduce the amine partner after activation.
• DBCO moiety generally tolerates neutral aqueous conditions; avoid prolonged exposure to strong nucleophiles or bases that could degrade linkages.

Target Specificity

Not applicable. This product is a small-molecule bioconjugation reagent and does not possess antigen/epitope specificity, clone, or isotype attributes.

Foire aux questions

How should this product be stored?

Store at ?20 °C. Freezer storage is required to maintain the specified shelf life.

How is this product shipped?

This product ships in an insulated container with ice pads. Unpack on arrival and transfer it to the storage condition stated above.

What are the CAS number, molecular formula and molecular weight?

The CAS Number is D1445666, the molecular formula is C26H28N2O6, and the molecular weight is 464.51 g/mol.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.