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

概要

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

仕様と純度

≥98%

保管条件

Store at -20°C

入荷

Ice chest + Ice pads

この製品は冷冷この冷このこの製品の運送が必要です。地上およびその他の経済サービスは利用できません。

純度

≥98%

化学的性質と物理的性質

• 溶解度: 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.