DBCO-PEG3-amide-N-Fmoc , CAS No.D1445675

CAS: D1445675 Cat. No.: D1445675 Formule: C₄₁H₄₂N₄O₇ Poids moléculaire: 702.79

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Vue d’ensemble

DBCO-PEG3-amide-N-Fmoc is a PEG-based PROTAC linker that can be used in the synthesis of PROTACs. DBCO-PEG3-amide-N-Fmoc 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

702.79

Application Protocols

Item-specific, validated protocols are not provided for this entry. The following literature-style procedures illustrate typical use; adjust to your system.

• SPAAC conjugation to an azide-labeled protein (general)

  1. Prepare protein (e.g., 10–50 μM) in PBS, pH 7.4. Optionally include 5–10% DMSO to aid solubility.
  2. Dissolve DBCO-PEG3-amide-N-Fmoc in anhydrous DMSO (10–50 mM stock). Add to protein to achieve 2–5 equiv.
  3. Incubate at room temperature for 1–2 h with gentle mixing. Monitor by LC–MS or SDS-PAGE with UV visualization as applicable.
  4. Desalt by spin column or dialysis to remove excess small molecule.

• Incorporation into a peptide via SPPS (Fmoc)

  1. Swell resin in DMF; perform standard Fmoc deprotection.
  2. Couple the reagent using HATU (or HBTU)/DIPEA in DMF (1.5–3 equiv, 10–30 min).
  3. Continue chain elongation as needed. Retain Fmoc if the amine must remain protected; otherwise deprotect with 20% piperidine in DMF.
  4. Cleave peptide and purify by RP-HPLC; perform SPAAC with azide partner in aqueous buffer.

• Notes

  • Keep solutions dry and neutral to preserve Fmoc and DBCO integrity.
  • Validate stoichiometry and time for your substrate; scale carefully from screening to preparative runs.

Biological Roles

This reagent is a synthetic linker for research bioconjugation and does not possess an intrinsic biological role or therapeutic function. The notes below contextualize how its chemical features interface with biomolecules (literature/general guidance).

• Bioorthogonal reactivity

  • The DBCO moiety undergoes strain-promoted azide–alkyne cycloaddition (SPAAC) with azide-functional biomolecules (proteins, glycans, nucleic acids, lipids), forming a stable triazole without metal catalysts. This reaction proceeds in complex media and is minimally perturbing to biological systems.

• PEG3 spacer

  • Short PEG segments enhance aqueous compatibility, reduce nonspecific hydrophobic interactions, and can improve conjugation efficiency by distancing DBCO from the macromolecular surface.

• Fmoc-amine handle

  • Enables site-specific introduction into peptides during SPPS, positioning the DBCO for downstream conjugation to azide-bearing probes or carriers.

• Stability considerations in biological contexts

  • The triazole formed after SPAAC is metabolically robust and resists hydrolysis and redox processes. Prior to reaction, the strained alkyne can be slowly quenched by strong nucleophiles or thiol–yne pathways under forcing conditions; neutral, aqueous buffers minimize side reactions.

• Applications (research use only)

  • Tracking, imaging, and capture workflows where an azide partner has been installed enzymatically or chemically on the target biomolecule.

Buffer Applications

This product is not a buffering agent and is not used to control pH. However, it is commonly employed in aqueous buffers as a coupling partner in SPAAC reactions (literature guidance).

• Typical buffers for SPAAC

  • Phosphate-buffered saline (PBS), HEPES, or Tris buffers at pH 6.5–8.0 with 5–20% DMSO or DMF co-solvent to maintain solubility of hydrophobic partners.
  • Avoid strong basic buffers if Fmoc protection must be retained; piperidine-containing mixtures will remove Fmoc.

• Practical tips

  • Degassing is not required for SPAAC (no metal catalyst). Include salts and stabilizers compatible with the biomolecule. Filter buffers (0.22 μm) to reduce particulates prior to conjugation.

Green Alternatives

Green chemistry considerations focus on solvent selection, copper-free click strategy, and minimizing hazardous reagents while maintaining performance.

• Copper-free advantage (literature)

  • SPAAC with DBCO avoids copper catalysts used in CuAAC, eliminating Cu removal burdens and potential biomolecule damage. This reduces metal waste and simplifies aqueous bioconjugation.

• Solvent choices and trade-offs

  • Favor water-rich media with minimal DMSO/DMF co-solvent where solubility allows. Optimize concentration to keep co-solvent ≤10–20%.
  • Where possible, substitute:
    • Replace dichloromethane with 2-MeTHF or ethyl acetate for workups and extractions.
    • Use ethanol or isopropanol for precipitation/purification where compatible.

• Comparison (general guidance)

  • DMF vs NMP vs DMSO
    • DMF: Lower viscosity, effective for SPPS; regulatory scrutiny as a reproductive toxin—control exposure and waste.
    • NMP: Similar concerns as DMF; assess EHS profile.
    • DMSO: Better EHS profile but can enhance dermal absorption—use PPE.

• Process intensification

  • Perform SPAAC at ambient temperature, reducing energy consumption.
  • Employ aqueous buffer systems and on-resin transformations when feasible to minimize solvent use.

• Waste minimization

  • Plan orthogonal sequences (Fmoc deprotection then SPAAC or vice versa) to avoid rework and additional purification cycles. Recover and recycle acetonitrile in HPLC where facility permits.

Pharmaceutical Uses

No clinical or therapeutic claims are made. This reagent is intended for research use only.

In pharmaceutical R&D and manufacturing process development (general guidance):

• Conjugation/process intermediates

  • Serves as a copper-free click handle to construct conjugates to azide-bearing payloads, linkers, or surfaces under mild conditions, facilitating impurity control and avoiding copper removal steps.

• Peptide/protein derivatization

  • Incorporated during SPPS via its Fmoc-protected amine to furnish peptides ready for late-stage SPAAC to drugs, dyes, or polymers in formulation studies.

• Analytical development

  • Strong UV chromophores (DBCO/Fmoc aromatics; literature) aid HPLC method development and in-process control (IPC) for conjugation progress.

• Manufacturability considerations

  • Copper-free conditions simplify scalability for sensitive biologics. PEG3 length balances aqueous handling with minimal impact on hydrophobic interactions, which can be advantageous for purification and formulation screening.

Item-specific pharmacopeial status or excipient listings are not provided; refer to CoA/Spec Sheet and internal quality assessments for GMP suitability decisions.

Physical Properties

Item-specific physicochemical specifications have not been provided for this catalog entry. Values below are general/literature expectations for similar DBCO–PEGn–amide–Fmoc constructs and should be used as guidance only.

• 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 and formula: Not specified for this item; refer to CoA/Spec Sheet.
• Solubility (literature/guidance)
  • Highly soluble in polar aprotic organic solvents (DMF, DMSO, NMP, dichloromethane, acetonitrile).
  • Limited solubility in water; PEG3 improves dispersion, and aqueous mixtures (e.g., DMF/H2O, DMSO/H2O, PBS with co-solvent) are commonly used for SPAAC.
• LogP (qualitative, literature): Amphiphilic; the DBCO and Fmoc aromatics increase hydrophobicity while PEG decreases it. Overall moderate hydrophobicity with improved aqueous compatibility relative to non-PEGylated DBCO.
• pKa (relevant functional groups; literature): Fmoc-protected amine is non-basic; after deprotection, the primary amine would display typical aliphatic amine basicity (pKa ~9–10, literature). No acidic functionality expected aside from carbamate/amide (non-ionizing in neutral range).
• Thermal behavior (general): Fmoc carbamates are base-labile and can undergo elimination under strong base/heat. DBCO cyclooctynes can slowly isomerize or degrade at elevated temperature; store cold per item guidance.
• UV characteristics (literature): Strong aromatic absorption from Fmoc (λmax ~260–300 nm) and DBCO aromatic rings; useful for UV monitoring, but specific ε not provided for this item.

Quality and Grades

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

• Interpreting common grades (general guidance)

  • Research grade: Suitable for general synthetic/bioconjugation work; purity typically verified by NMR/LC–MS/HPLC but may not meet stringent pharmaceutical monographs.
  • HPLC grade/bioconjugation grade (when offered): Emphasis on low nonvolatile residue, tight control of residual solvents, and analytical traceability to support conjugation efficiency and downstream analytics.
  • Peptide synthesis grade: Low water content, low inorganic contaminants, and specifications on residual piperidine/diisopropylcarbodiimide byproducts; optimized for SPPS.

• Stabilizers/additives

  • Not specified for this item; refer to CoA/Spec Sheet.
  • General note: DBCO derivatives typically require no stabilizer; quality is preserved by dry, cold, and dark storage.

• Documentation and traceability

  • For release decisions, rely on the item’s CoA for assay/purity method (e.g., HPLC area%), identity (NMR/HRMS), and residual solvent/water. Where critical to process development, request impurity profiles and lot-specific water content.

Reaction and Applications

DBCO-PEG3-amide-N-Fmoc unites copper-free click reactivity with peptide-compatible protection, enabling modular workflows from solid-phase peptide synthesis (SPPS) to late-stage bioconjugation.

• Key application areas (literature)

  • SPAAC bioconjugation: Rapid, catalyst-free cycloaddition with organic azides on small molecules, polymers, oligonucleotides, and biomacromolecules. PEG3 spacing reduces steric hindrance and improves aqueous handling.
  • Peptide diversification: The Fmoc-protected amine allows incorporation during SPPS, positioning a DBCO handle within a peptide for subsequent conjugation to azide-bearing cargos (dyes, affinity tags, polymers, ADC linkers—research use).
  • Surface functionalization: Immobilization on azide-terminated surfaces (or vice versa) to build click-ready materials.

• Practical notes

  • Kinetics: SPAAC is typically fast at ambient temperature; rate increases with concentration and in less polar media. PEG improves accessibility in aqueous media.
  • Orthogonality: Fmoc protection is orthogonal to SPAAC. Conduct SPAAC under neutral conditions; perform Fmoc deprotection separately with base only when desired.
  • Analytics: Monitor reaction progress by LC–MS or HPLC-UV using Fmoc/DBCO absorptions; confirm triazole formation by MS (+N2 mass increment for azide addition; literature concept).

• Related transformations (literature)

  • Sequential ligations: Combine SPAAC with thiol–maleimide coupling or oxime ligation in orthogonal sequences.
  • Resin-to-solution connectivity: Attach DBCO during SPPS, cleave peptide, then perform SPAAC in solution to sensitive biomolecules without Cu catalysts.

Reaction Conditions

The following are literature-based general conditions for similar DBCO–PEG–Fmoc reagents; optimize for your specific substrates.

• SPAAC (DBCO + azide)

  • Solvent: Aqueous buffers (PBS, HEPES) with 5–20% DMSO or DMF; purely organic media (DMF, DMSO, ACN) for small molecules.
  • Concentration: 10–1000 μM for biomolecules; 1–50 mM for small-molecule couplings.
  • Temperature: 20–25°C (ambient). Cooler temperatures preserve biomolecule integrity; mild heating (30–37°C) can accelerate sluggish reactions.
  • Stoichiometry: 1.2–5.0 equiv of the limiting partner to drive to completion; excess DBCO may be quenched with a small azide scavenger if needed.
  • Time: Minutes to a few hours depending on concentration and sterics; monitor by LC–MS/HPLC.
  • pH: Neutral (6.5–8.0) to maintain biomolecule stability and avoid Fmoc loss.

• Incorporation via SPPS (Fmoc strategy)

  • Coupling: HATU/HBTU or DIC–Oxyma in anhydrous DMF/NMP, 1.5–3.0 equiv reagent, 5–30 min contact, ambient.
  • Fmoc deprotection: 20% piperidine in DMF, 2×(5–10 min) cycles; minimize exposure to avoid side reactions on sensitive sequences. If retention of Fmoc is desired, exclude base during other operations.

• Workup/purification

  • For small molecules: Preparative RP-HPLC (water/ACN with 0.1% formic acid or TFA). For peptides: standard cleavage and purification protocols post-SPPS, then SPAAC in solution.

Safety and Handling

• GHS/SDS

  • Signal word: Not specified for this item; refer to SDS.
  • Hazard statements and pictograms: Not specified for this item; refer to SDS.
  • Always consult the product SDS for authoritative hazard, toxicological, and regulatory information.

• General laboratory precautions (best practice for DBCO/Fmoc reagents)

  • PPE: Lab coat, safety glasses, and appropriate chemical-resistant gloves (e.g., nitrile). Handle in a chemical fume hood to avoid inhalation of dust or vapors from solvents (DMF/DMSO/DCM) used for dissolution.
  • Avoid contact with skin/eyes; wash thoroughly after handling.
  • Incompatibilities: Strong bases can remove Fmoc. Strong nucleophiles or radical/photochemical conditions can add to alkynes. Azide-bearing materials will react by SPAAC—segregate intentionally functionalized azide reagents/surfaces.
  • Peroxide formation: Not applicable to this solid reagent itself; however, many organic solvents used (ethers) can form peroxides—follow solvent SOPs.

• Reactivity notes (literature guidance)

  • DBCO is a strained alkyne and will undergo rapid, exothermically favorable cycloaddition with organic azides; avoid unintended exposure to azide-containing reagents.
  • Fmoc group is base-labile; avoid piperidine, morpholine, or DBU unless deprotection is intended.

• First aid (general)

  • Skin/eye contact: Rinse with water for at least 15 minutes. Remove contaminated clothing. Seek medical attention per SDS.
  • Inhalation/ingestion: Move to fresh air; seek medical attention. Provide SDS to healthcare personnel.

Solvent Selection

This reagent is an amphiphilic, aromatic–PEGylated solid. Solvent choice impacts dissolution rate, reaction kinetics (SPAAC), and compatibility with biomolecules.

• Miscibility and polarity (literature guidance)

  • Preferred: DMF, DMSO, NMP, dichloromethane, acetonitrile. These dissolve DBCO-PEG constructs rapidly at mg–mL−1 levels.
  • Aqueous systems: Use co-solvent strategies (5–30% DMSO or DMF in PBS, HEPES, or saline) for bioconjugations with azide-functional biomolecules. PEG3 improves compatibility vs non-PEGylated DBCO.
  • Alcohols: MeOH/EtOH can dissolve; ensure stability of the Fmoc carbamate (avoid basic alcoholates).

• Selection tips

  • SPAAC with biomolecules: Start with aqueous buffers containing 10–20% DMSO or DMF to maintain protein stability while keeping DBCO in solution.
  • SPPS workflows: Use anhydrous DMF or NMP for coupling; DCM for resin swelling when appropriate.
  • Purification: Reverse-phase HPLC (water/ACN with 0.1% TFA or formic acid) is common; DBCO/Fmoc absorb in UV, aiding detection.

• Comparison (guidance)

  • DMF vs DMSO: DMF gives lower viscosity and is favored for SPPS; DMSO offers better biocompatibility and is frequently used in aqueous SPAAC.
  • ACN: Useful for LC and precipitation control but may offer weaker solvation for PEGylated aromatics compared to DMF/DMSO.

All solvent choices should be validated for your specific substrate and process; avoid strong base if Fmoc retention is required.

Storage and Reconstitution

• Item-specific storage and shipping

  • Storage Conditions: Store at -20°C.
  • Shipped In: Ice chest + Ice pads.

• General handling guidance (literature/best practice)

  • Protect from moisture and prolonged light exposure; many DBCO derivatives and Fmoc carbamates benefit from desiccated, light-protected storage.
  • Warm to room temperature in a desiccator before opening to prevent condensation. Reseal promptly under dry inert gas if possible.

• Reconstitution (general)

  • Dissolve in anhydrous DMF or DMSO to prepare concentrated stocks (e.g., 10–50 mM). Filter through 0.22 μm PTFE if particulates are present.
  • For aqueous applications, dilute stock solutions into buffer (PBS/HEPES) to the desired final concentration, maintaining 5–20% organic co-solvent if needed for solubility.

• Aliquoting and stability

  • Prepare single-use aliquots and store at -20°C to minimize freeze–thaw. Avoid repeated exposure to base if Fmoc integrity is required.

• Disposal

  • Dispose of unused solutions and contaminated materials according to institutional and local regulations for organic chemicals and amide/PEGylated compounds.

Refer to the product’s CoA/Spec Sheet and SDS for any lot-specific recommendations or constraints beyond the general guidance above.

Structure and Identity

DBCO-PEG3-amide-N-Fmoc is a multifunctional, copper-free click chemistry building block that combines a strained cyclooctyne (DBCO), a short hydrophilic spacer (PEG3), an amide linkage, and an Fmoc-protected amine handle for peptide chemistry.

• Item-specific identifiers

  • 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.

• Structural features (general description based on name; literature)

  • DBCO motif: A dibenzocyclooctyne ring system featuring a highly strained cycloalkyne fused to two benzene rings; enables strain-promoted azide–alkyne cycloaddition (SPAAC) without Cu catalysts.
  • PEG3 spacer: Three ethylene glycol units (–CH2–CH2–O–)3 impart water compatibility, reduce hydrophobic aggregation, and increase linker reach between conjugation partners.
  • Amide linkage: Provides hydrolytically robust connectivity between the PEG chain and the Fmoc-protected amine.
  • N-Fmoc protecting group: Fluorenylmethyloxycarbonyl carbamate protecting group on the terminal amine, base-labile under standard Fmoc deprotection conditions (e.g., piperidine in DMF; literature).

• 2D structural description (general)

  • An aromatic–aliphatic hybrid where a dibenzofused cyclooctyne ring is tethered via a short PEG chain to an amide, terminating in an Fmoc carbamate-protected amine. No defined stereocenters are expected; the strained alkyne is embedded in the cyclooctyne ring.

Synthetic Utility

DBCO-PEG3-amide-N-Fmoc is a versatile synthetic linchpin enabling orthogonal assembly of complex architectures.

• Functional group reactivity (literature)

  • Strained alkyne (DBCO): Rapid [3+2] cycloaddition with organic azides (SPAAC) forming 1,2,3-triazoles without metal catalysts. Orthogonal to many peptide-side-chain protections.
  • Fmoc-protected amine: Incorporated onto resins or carboxyl-bearing partners using standard amide coupling (e.g., HATU/HBTU/DIC–Oxyma). Fmoc removed with secondary amines (piperidine) under SPPS protocols.
  • Amide/PEG segment: Chemically robust spacer conferring flexibility and solvating power.

• Retrosynthetic value

  • Enables a two-stage build: install the DBCO-bearing unit in a peptide or small molecule, then perform modular late-stage ligation to any azide partner, decoupling synthesis of the two halves.

• Downstream transformations

  • After SPAAC, the resultant triazole is stable to acids, bases (moderate), and hydrogenation, supporting orthogonal post-modifications on remaining handles (e.g., thiols, amines, maleimides on the counterpart).

• Purification and analytics

  • UV-active Fmoc/DBCO facilitate HPLC monitoring; LC–MS provides clear mass shifts upon triazole formation (+N3–N2 net addition; literature concept). Reverse-phase methods are typical for small-molecule/peptide conjugates.

Target Specificity

Not applicable. This product is a small-molecule linker for chemical conjugation and does not have biological target specificity (no antigen, epitope, clone, or isotype). For selectivity in use, rely on the bioorthogonal nature of SPAAC toward azide-functionalized partners.

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 D1445675, the molecular formula is C41H42N4O7, and the molecular weight is 702.79 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.