DBCO-C3-PEG4-amine - ≥98%

Cat. No.: D597220

GRADE & PURITY ≥98%

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Application

227,228,229

Vue d’ensemble

DBCO-C3-PEG4-amine is a PEG derivative which contains DBCO and amine moieties. The DBCO group is commonly used in copper-free Click Chemistry reactions. The amine group is reactive with carboxylic acids, activated NHS esters, carbonyls (ketone, aldehyde) etc. The hydrophilic PEG spacer increases solubility in aqueous media.

Specifications

Spécifications et pureté

≥98%

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.

Pureté

≥98%

Propriétés chimiques et physiques

• Solubilité: Solubility in DMSO, DCM, DMF

Application Protocols

The following protocols are general, literature-based examples intended to help plan experiments. They are not item-specific validated procedures.

• Protocol A: SPAAC labeling of an azide-modified protein

  1. Dissolve DBCO-C3-PEG4-amine at 10–50 mM in anhydrous DMSO.
  2. Prepare protein (with azide handles) in PBS or HEPES, pH 7.4, 0.5–2 mg/mL; ensure buffer is free of sodium azide.
  3. Add DBCO stock to reach 5–20× molar excess over estimated azide sites; keep DMSO ≤5% v/v.
  4. Incubate 1–4 h at RT (or overnight at 4°C). Gently mix.
  5. Quench excess with an azide scavenger (optional) or remove by desalting (SEC spin column) or dialysis.
  6. Analyze by LC–MS, SDS-PAGE, or functional assay.

• Protocol B: Installing DBCO onto a carboxylated small molecule via NHS ester

  1. Activate the acid (on the small molecule) with NHS/DIC (or EDC/NHS) in dry DMF (0–25°C, 1 h).
  2. Add DBCO-C3-PEG4-amine (1.2–2.0 equiv) and DIPEA (1–2 equiv). Stir at RT for 2–4 h.
  3. Monitor by LC–MS/HPLC. Upon completion, quench, concentrate, and purify by preparative HPLC.

• Protocol C: EDC/NHS coupling to a carboxylated surface

  1. Activate surface with EDC/NHS in MES, pH 5.5, 15–30 min.
  2. Rinse, then add DBCO-C3-PEG4-amine in phosphate buffer, pH 7.8–8.2 (0.1–2 mM), 1–2 h.
  3. Rinse thoroughly; block residual active esters with ethanolamine.
  4. Proceed with SPAAC attachment of azide-labeled ligands.

Adjust times, equivalents, and temperatures to suit your substrates.

Biological Roles

This product is a synthetic bioconjugation linker; it does not have intrinsic biological activity or roles. The following describes its function as a chemical tool in biochemical systems (research use only).

• Bioorthogonal reactivity

  • SPAAC proceeds without interacting with native cellular functional groups, allowing selective reaction with azide tags introduced metabolically or by prior derivatization (literature concept of bioorthogonality).

• Linker design

  • PEG4 segment enhances aqueous compatibility and can reduce nonspecific binding by increasing hydrophilicity and providing conformational flexibility.
  • C3 aliphatic spacer adds short hydrophobic separation from the DBCO core, balancing reach and compactness.

• Bioconjugation roles

  • Installation of DBCO on proteins, peptides, oligonucleotides, carbohydrates, lipids, and materials via the terminal primary amine (e.g., amide coupling to carboxylates), followed by selective reaction with azide-bearing counterparts.
  • Creation of defined constructs for imaging, pull-down assays, proximity labeling tools, and surface passivation/functionalization in biosensing.

• Considerations

  • Avoid buffers containing sodium azide, which will consume DBCO.
  • Degree of labeling and site distribution should be assessed (MS, UV/Vis, fluorophore response) to correlate with function.
  • PEG-containing linkers can reduce aggregation and may influence hydrodynamic radius of conjugates, affecting separation (SEC) and electrophoretic mobility (general observation).

No therapeutic or clinical uses are implied; this material is for laboratory research and development.

Buffer Applications

DBCO-C3-PEG4-amine is commonly used in aqueous buffers for SPAAC reactions and in mildly basic buffers for amide couplings involving its primary amine.

• General SPAAC buffer conditions (literature guidance)

  • Buffer types: PBS, HEPES, or phosphate buffer, pH 6.8–7.8.
  • Additives: 0.01–0.1% nonionic surfactant (e.g., Tween-20) if needed to stabilize conjugates; avoid surfactant if it sequesters hydrophobic partners.
  • Critical caution: Do not use sodium azide as a preservative; it will react with DBCO. Use alternatives (e.g., ProClin) if compatible with the system.

• Amide coupling using the terminal amine

  • Conduct coupling to NHS-esters or activated carboxyls in amine-free buffers (e.g., 50 mM phosphate, pH 7.2–7.8) or in organic media (dry DMF) with subsequent buffer exchange.
  • For EDC/NHS activation on surfaces or carboxylated biomolecules, use MES buffer (pH 5.0–6.5) for activation, then add the amine linker in phosphate or borate buffer pH 7.5–8.5 for coupling.

• Practical recipes (example scales)

  • Prepare a 10–50 mM DBCO-linker stock in DMSO; add to buffer to achieve 10–100 µM final (for labeling) while keeping DMSO ≤5% v/v.
  • Use molar excesses of 1.2–5× over azide sites depending on accessibility; monitor completion by MS or azide-specific assays.

Optimize ionic strength and pH for the biomolecule of interest to balance reactivity with structural integrity.

Green Alternatives

DBCO-C3-PEG4-amine enables copper-free SPAAC, which can be greener and more biocompatible than Cu-catalyzed azide–alkyne cycloaddition (CuAAC), especially by eliminating copper salts and reducing chelator waste.

• Comparative overview (general, literature)

| Approach | Catalyst/Metal | Typical solvent | Aqueous compatibility | Waste considerations | Notes | |---|---|---|---|---|---| | SPAAC with DBCO | None | Buffer ± small % DMSO/DMF | Excellent | Minimal metal waste | Larger reagent MW; strained alkyne synthesis upstream has footprint | | CuAAC (alkyne + azide) | Cu(I)/Cu(II) + ligand | t-BuOH/H2O or H2O + ligand | Good | Copper/ligand waste; quench required | High kinetics; possible cytotoxicity of Cu in live systems | | iEDDA (Tz–TCO) | None | Buffer | Excellent | Minimal | Fastest kinetics; requires tetrazine/TCO partners |

• Solvent best practices with this product

  • Favor aqueous buffers with minimal DMSO/DMF co-solvent.
  • Use acetone or ethanol for equipment rinsing instead of chlorinated solvents when compatible.

• Process considerations

  • Conduct reactions at ambient temperature to reduce energy input.
  • Employ microscale stoichiometry optimization to minimize excess linker.
  • Consider recyclable solid supports bearing azide/DBCO to simplify purification and reduce solvent use.

Trade-offs: DBCO reagents may have higher embodied synthesis impact versus simple alkynes; however, they avoid copper catalysts and enable milder, often water-based processes that reduce downstream purification burden.

Pharmaceutical Uses

No clinical or therapeutic claims are made. In pharmaceutical R&D and manufacturing contexts, DBCO-C3-PEG4-amine may serve the following roles as a research reagent or process intermediate:

• Bioconjugation intermediate in the preparation of investigational conjugates (e.g., antibody, peptide, oligonucleotide, or polymer constructs) where azide counterparts are present.
• Surface functionalization of analytical devices or particles used in bioassays (e.g., DBCO-display on solid supports for capture of azide-bearing analytes).
• Payload attachment studies in preformulation and analytical method development, assisting in the evaluation of linker stability, hydrophilicity effects (from PEG4), and conjugation stoichiometry.
• Reference/analytical standard for method development (HPLC/UPLC, LC–MS) to establish retention and detection parameters for DBCO-bearing moieties in complex mixtures.

Pharmacopeial status, excipient monographs, and GMP suitability are not specified for this item; refer to your QA/QC requirements and the product CoA/Spec Sheet if regulated use is contemplated. Typically, such linkers are employed in discovery and early development workflows under research-use-only provisions.

Physical Properties

Item-specific physicochemical specifications are not provided; refer to the CoA/Spec Sheet for authoritative values.

• Item-specific data

  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
  • Melting point, boiling point, density, refractive index, water content, residual solvents, UV cutoffs: Not specified for this item; refer to CoA/Spec Sheet.

• General/literature characteristics for DBCO–PEGn–amines (informational)

  • Physical state: typically off-white to light-colored solid; amorphous or low-melting waxy solid depending on salt form and hydration.
  • Solubility profile: readily soluble in polar aprotic solvents (DMSO, DMF, NMP); soluble to moderately soluble in alcohols (MeOH, EtOH) and aqueous buffers when pre-dissolved in DMSO/DMF; aqueous solubility increases with protonation (e.g., HCl salt) and presence of PEG segment (literature).
  • Partitioning: PEG spacer reduces lipophilicity versus hydrocarbon linkers; DBCO ring retains hydrophobic character, so mixed aqueous/organic systems are often used.
  • Stability: DBCO is generally stable at low temperature; slowly reacts with azides; susceptible to nucleophilic attack under strongly basic conditions and can be oxidatively sensitive; protect from prolonged light and air exposure (general practice).
  • pKa (terminal amine): primary aliphatic amine typically pKa ~9–10 (literature, depends on neighboring PEG/aryl context). Protonation aids water solubility for handling.

These properties are provided as general guidance; actual item behavior may vary with counterion, residual solvent, and lot. Always verify with small-scale tests.

Quality and Grades

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

• Interpreting typical grades for bioconjugation linkers (general guidance)

  • Bioconjugation/Linker grade commonly implies high chemical purity, low residual solvents, and low inorganic/metallic impurities to ensure clean coupling and minimal background in bioassays.
  • HPLC-grade or >95% purity (literature context) is often sought to minimize side products in SPAAC or amide couplings; UV-trace impurities can interfere with quantification.
  • Salt form (free base vs. HCl salt) impacts handling and solubility; confirm on the CoA to plan dissolution and pH adjustments.

• Stabilizers/additives

  • DBCO derivatives generally do not require stabilizers; however, they benefit from dry, oxygen- and light-minimized storage. Any stabilizers present would be listed on the CoA/SDS. Not specified for this item; refer to CoA/Spec Sheet.

• Lot-specific QC typicals (informational)

  • Identity verification by NMR and HRMS, purity by HPLC/UPLC, residual solvents by GC, and water by Karl Fischer are standard for this class of reagent (literature/common practice). Actual tests and limits for this SKU are not specified; refer to CoA.

• Practical note

  • For sensitive bioconjugations or materials work, request the latest CoA/Spec Sheet to confirm purity, salt form, and residuals before scaling protocols or preparing standards.

Reaction and Applications

DBCO-C3-PEG4-amine enables orthogonal bioconjugation through two handles: a SPAAC-ready strained alkyne and a primary amine for amide/urea/carbamate formation.

• Strain-promoted azide–alkyne cycloaddition (SPAAC)

  • Copper-free click with organic azides on biomolecules, polymers, surfaces, nanoparticles, and probes.
  • Proceeds under physiological conditions (aqueous buffers, pH ~6–8, RT), compatible with living systems in research settings (no Cu catalyst required; literature).
  • PEG4 spacer reduces steric hindrance and can improve reaction reach on crowded biomolecular surfaces.

• Amine-directed coupling

  • Amide formation with NHS esters, anhydrides, or carbodiimides (EDC/HOBt, DIC) to install DBCO functionality onto carboxyl-bearing substrates.
  • Urea/carbamate formation via isocyanates or activated carbonates for polymer modification.
  • Support immobilization on carboxylated resins/particles to create DBCO-functionalized affinity matrices.

• Orthogonal assembly strategies

  • Sequentially couple the amine to a target (e.g., protein carboxyls) then perform SPAAC with an azide-tagged payload, or vice versa using azide-first strategies on the counterpart.

• Application areas (research use only)

  • Site-selective bioconjugation, antibody/oligonucleotide labeling (via azide counterparts), hydrogel functionalization, surface patterning, and bio-orthogonal imaging probe assembly.

• Practical tips

  • Keep solutions free of sodium azide and minimize competing nucleophiles during NHS couplings.
  • Use modest bases (e.g., DIPEA) and avoid prolonged strong base exposure which can degrade strained alkynes.
  • Validate degree of labeling by UV/Vis, MS, or azide consumption assays.

Reaction Conditions

The following are literature-based, general conditions for reactions enabled by DBCO-C3-PEG4-amine. Actual optimal conditions depend on substrates; verify experimentally.

• SPAAC with azides

  • Solvent: aqueous buffers (PBS, HEPES) with 0–10% DMSO/DMF.
  • Concentrations: 10–100 µM for biomolecule labeling; 0.5–10 mM for small-molecule/polymer coupling.
  • Stoichiometry: 1.2–5.0 equivalents of DBCO-linker per azide site to drive to completion depending on accessibility.
  • Temperature: 20–25°C typically; 4°C possible with longer times; 37°C for faster kinetics if biomolecule stable.
  • Time: minutes to a few hours for small molecules; 1–16 h for crowded biomolecular sites (literature variability).
  • pH: 6.0–8.0. Avoid azide-containing preservatives.

• Amide coupling via terminal amine

  • With NHS esters: dry DMF or aqueous buffer (amine-free), pH 7.5–8.5; base such as DIPEA (0.5–2 equiv). RT for 1–4 h.
  • EDC/NHS activation (on carboxyl substrates): activate in MES buffer (pH 5–6); add amine linker in phosphate/borate pH 7.5–8.5; RT to 25–37°C, 0.5–4 h.
  • Carbonate/isocyanate couplings: anhydrous organic solvent (DCM, DMF); tertiary amine base; 0–25°C, 1–12 h.

• Workup/purification

  • Remove organic co-solvents under reduced pressure at ≤30°C; desalting via spin columns or SEC for proteins; HPLC for small molecules.
  • Monitor by LC–MS, SDS-PAGE (for proteins), or azide depletion assays.

• Stability considerations

  • Minimize exposure to strong base and high temperatures; protect from light and oxygen when feasible.

These conditions are guidance, not item-specific specifications.

Safety and Handling

Always consult the product SDS for definitive safety information. The following guidance reflects general best practices for DBCO-PEG amine linkers.

• GHS classification and hazard statements for this specific item: Not specified for this item; refer to SDS.

• Signal word/pictograms: Not specified for this item; refer to SDS.

• Key hazards (general)

  • Chemical reactivity: DBCO reacts rapidly with azides (SPAAC). Avoid unintended exposure to azide-containing reagents, preservatives (e.g., sodium azide), or azide-functionalized surfaces.
  • Irritation/sensitization: Many amine-containing and PEGylated linkers may cause skin/eye irritation. Handle as potentially irritating.
  • Dust/particulate: Avoid inhalation of powders. Use containment during weighing.

• PPE and engineering controls

  • Wear lab coat, safety glasses, and nitrile gloves; consider double-gloving when working with concentrated solutions.
  • Handle in a fume hood or ventilated enclosure, especially when weighing or dissolving.

• Storage and incompatibilities

  • Store at −20°C as specified; keep tightly closed, desiccated, and preferably protected from light.
  • Avoid azides, strong bases (which can degrade strained alkynes), strong oxidizers, and reactive acylating agents unless under controlled reaction conditions.

• First-aid overview (general)

  • Skin/eye contact: Rinse with water for ≥15 min; remove contaminated clothing; seek medical advice.
  • Inhalation: Move to fresh air; seek medical attention if symptoms persist.
  • Ingestion: Rinse mouth; do not induce vomiting; seek medical attention.

• Spill/waste

  • Absorb with inert material; collect for disposal. Dispose according to institutional and local regulations.

Solvent Selection

This product is a solid linker; solvent selection concerns dissolution for conjugation or coupling.

• Polarity/miscibility (general for DBCO–PEG amines)

  • Highly soluble: DMSO, DMF, NMP.
  • Moderately soluble: methanol, ethanol, acetonitrile; aqueous buffers when pre-dissolved as concentrates in DMSO/DMF.
  • Limited solubility: purely nonpolar solvents (hexanes, toluene) due to PEG segment.

• Recommended dissolution strategies

  • Prepare a concentrated stock (e.g., 10–50 mM) in anhydrous DMSO or DMF; filter if necessary through 0.22 µm PTFE.
  • For aqueous use, slowly add the organic stock into vigorously stirred buffer to final organic content ≤5–10% v/v to avoid precipitation.
  • For amide coupling (using the terminal amine), employ dry DMF or DCM:DMF mixtures with carbodiimide or activated ester chemistry; keep bases mild to preserve the cyclooctyne.

• Buffer compatibility (see also Buffer Applications)

  • SPAAC tolerates most neutral buffers; avoid sodium azide (will consume DBCO) and surfactants that may sequester hydrophobic DBCO.
  • If the amine is to be coupled to an NHS ester, avoid amine-containing buffers (e.g., Tris, glycine) that compete.

• When to choose alternatives

  • If high aqueous solubility is required without organic co-solvent, consider longer PEG linkers (PEG6–PEG12, literature) or formulate as an acid salt. For strictly organic media, DCM/DMF blends can balance solubility and volatility.

Storage and Reconstitution

• Storage (item-specific)

  • Store at −20°C.
  • Shipped on ice chest + ice pads. Upon receipt, place immediately at −20°C.

• General handling guidance

  • Allow container to equilibrate to room temperature in a desiccator before opening to prevent moisture condensation.
  • Work quickly on the bench; keep the bulk material dry and protected from light.

• Reconstitution and stock solutions (general)

  • Dissolve in anhydrous DMSO or DMF to prepare 10–50 mM stocks. If needed, convert to aqueous buffer by slow dilution to ≤5–10% organic.
  • For applications requiring protonated amine (enhanced water solubility), adjust solution pH with compatible acid after dissolution or use an appropriate aqueous buffer.
  • Filter sterilize (0.22 µm PTFE) if sterile solutions are required and solvent is compatible.

• Aliquoting and freeze–thaw

  • Aliquot stock solutions into single-use volumes; store at −20°C.
  • Avoid repeated freeze–thaw; discard aliquots showing precipitation or discoloration.

• Stability notes (general)

  • Keep away from azides to prevent consumption of the DBCO moiety.
  • Limit exposure to strong bases and elevated temperatures that can degrade strained alkynes.

For any lot-specific stability, purity, or solubility details, consult the current CoA/Spec Sheet and SDS.

Structure and Identity

DBCO-C3-PEG4-amine is a bifunctional, strain-promoted click chemistry/bioconjugation linker combining a dibenzocyclooctyne (DBCO) handle with a short aliphatic (C3) and PEG4 spacer terminating in a primary amine.

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

• Structural features (general, literature description)

  • DBCO (dibenzocyclooctyne): a fused bicyclic aryl system flanking an 8-membered cycloalkyne ring; the alkyne is highly strained and undergoes rapid strain-promoted azide–alkyne cycloaddition (SPAAC) with organic azides without Cu catalysts.
  • Spacer architecture: an aliphatic C3 propyl segment adjacent to a PEG4 (tetraethylene glycol) segment that enhances hydrophilicity and distance from surfaces/biomolecules, reducing steric hindrance.
  • Terminal functionality: a primary aliphatic amine (–NH2) enabling amide formation with activated carboxyls (e.g., NHS esters), carbamate/urea formation with activated carbonates/isocyanates, or immobilization on carboxylated matrices.
  • 2D description: Aromatic–cyclooctyne core on one end; a short propyl tether leading into four ethylene glycol repeats; terminal –CH2–CH2–CH2–O–(CH2–CH2–O)4–CH2–CH2–NH2 motif (schematic, representative) linking the reactive amine to the DBCO.

• Stereochemistry: No stereocenters in the linker; the cyclooctyne adopts conformations imposed by ring strain (literature).

Synthetic Utility

DBCO-C3-PEG4-amine is a versatile building block providing orthogonal reactivity and modular spacing.

• Functional groups and reactivity

  • Strained alkyne (DBCO): undergoes SPAAC with azides to yield stable triazole linkages; compatible with water and biological media (literature).
  • Primary amine: enables amide formation with activated carboxyls (NHS esters, anhydrides), urea formation with isocyanates, and carbamate formation with chloro/aryl carbonates.
  • PEG4 spacer: increases solubility and reduces aggregation; beneficial for transitioning between organic synthesis and aqueous bioconjugation.

• Retrosynthetic value

  • Serves as a DBCO donor to install SPAAC handles onto diverse scaffolds without introducing copper catalysis downstream.
  • Offers a short, defined linker length (C3+PEG4) to tune distance and flexibility between a core substrate and the DBCO moiety.

• Integration points

  • Attach the amine to carboxylated polymers, dyes (as NHS esters), nanoparticles, or small molecules; subsequently react with azide-functionalized partners to assemble higher-order constructs.
  • Alternatively, immobilize the amine on carboxylated resins to prepare DBCO-functionalized solid supports for flow or batch capture of azides.

• Practical notes

  • Maintain mild basic conditions (e.g., DIPEA, pH 7.5–8.5) for amide couplings; excessive base or prolonged heating can compromise the cyclooctyne.
  • Sequence planning: perform amide coupling first, purify, then conduct SPAAC to avoid side reactions with azide-bearing reagents during coupling steps.

Target Specificity

Not applicable. DBCO-C3-PEG4-amine is a general-purpose chemical linker with no inherent biological target, antigen, clone, or isotype. Its selectivity arises from bioorthogonal chemistry: it reacts specifically with organic azides (SPAAC) while the terminal amine reacts with activated carboxyls under controlled coupling conditions.