DBCO-PEG5-acid - ≥97%

Cat. No.: D596732

GRADE & PURITY ≥97%

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

DBCO-PEG5-acid is an analog of DBCO-Acid with PEG linker and a DBCO group. DBCO group is a highly reactive cycloalkyne which is commonly used for copper-free Click Chemistry reactions. The hydrophilic PEG chain allows for increased water solubility of compounds in aqueous media. The terminal carboxylic acid can be reacted with primary amine groups in the presence of activators (e.g. EDC, or DCC) to form a stable amide bond.

Specifications

Specifications & Purity

≥97%

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

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

Purity

≥97%

Chemical and Physical Properties

• Solubility: Solubility in DMSO, DCM, DMF

Application Protocols

No item-specific, validated application protocols are provided in the Product Data for this SKU. The following general procedures are offered as literature-style guidance only.

• SPAAC labeling of an azide-functionalized peptide/protein (typical):

  1. Dissolve DBCO-PEG5-acid (or a pre-formed DBCO-PEG5–NHS ester) at 10–50 mM in anhydrous DMSO. If using the acid directly for SPAAC, first couple the acid to the biomolecule via EDC/NHS to install DBCO; then perform SPAAC with the azide payload.
  2. Prepare the azide-bearing counterpart in PBS or HEPES, pH 7.2. Optional: include 2–5% DMSO.
  3. Mix to achieve 50–500 μM DBCO and 25–250 μM azide (2:1 molar ratio as a starting point). Incubate 1–2 h at room temperature.
  4. Purify by desalting (G-25), spin filtration, or RP-HPLC as appropriate. Confirm by LC-MS.

• Installation of DBCO onto amine-bearing polymer (small-molecule coupling):

  1. In dry DMF, combine DBCO-PEG5-acid (1.0 eq), NHS (1.2 eq), EDC·HCl (1.2 eq), and DIPEA (2.5 eq). Stir 30–60 min at 0–25 °C.
  2. Add the amine substrate (1.0 eq per activated ester), continue 2–12 h.
  3. Quench with ethanolamine or water. Work up and purify by precipitation or chromatography.

Note: Optimize stoichiometry, pH, and time for your system. For research use only.

Biological Roles

Scope note: DBCO-PEG5-acid is a synthetic bioconjugation reagent, not a natural metabolite. The following addresses its roles and behavior in biochemical workflows (no clinical/therapeutic claims).

• Bioorthogonal reactivity: The DBCO motif reacts selectively with organic azides via SPAAC, a transformation that is foreign to native biochemistry. This orthogonality enables labeling of azide-tagged glycans, lipids, nucleic acids, or proteins in complex biological matrices.
• Live-cell compatibility (literature/general): Copper-free conditions eliminate cytotoxic Cu(I), facilitating cell-surface labeling when azides are metabolically incorporated (e.g., Ac4ManNAz for sialic acids). DBCO-PEG linkers often show improved aqueous handling and reduced nonspecific binding compared to non-PEGylated analogs.
• Linker function: PEG5 adds hydrophilicity and spacing to reduce steric hindrance and mitigate hydrophobic interactions with membranes or proteins, potentially improving accessibility to azide sites.
• Downstream analytics: The triazole formed after SPAAC is chemically and enzymatically robust, supporting proteomics workflows (e.g., enrichment via biotin-azide capture after installing DBCO on a scaffold) or imaging when coupled to fluorophore-azides.
• Non-specific interactions: Despite PEGylation, the aromatic DBCO core can still associate with hydrophobic domains; titrate reagent equivalents to minimize off-target adsorption.

Caveat: Biological behavior (permeability, binding, toxicity) is formulation- and cell-type-dependent. For this SKU, no item-specific biological data are provided; consult the literature and perform preliminary toxicity/compatibility checks under your exact conditions.

Buffer Applications

Applicability: DBCO-PEG5-acid is not a classical buffering agent. However, it is frequently used in aqueous buffers for bioconjugation. The following provides practical guidance for preparing and using it in buffers (general/literature information).

• SPAAC in buffers:

  • Common buffers: PBS, HEPES, or phosphate buffer, pH 7.0–7.5. Avoid azide-containing buffers/preservatives which would quench the DBCO (e.g., sodium azide in PBS).
  • Co-solvent: 5–10% DMSO or DMF can aid dissolution without severely impacting most proteins; verify compatibility.

• EDC/NHS activation in aqueous media:

  • For amide coupling of the terminal acid to amines on proteins/surfaces, use MES buffer (50–100 mM, pH 5.0–6.0) for activation, then adjust to pH 7.0–7.4 for coupling; avoid primary amines (e.g., Tris) which compete with the desired amide formation.

• Concentration ranges (literature typical):

  • Protein labeling: 2–20 equivalents of DBCO-PEG5-acid relative to accessible amines when pre-activating to NHS ester; for SPAAC, use 1.2–5 equivalents relative to azide sites.

• Practical notes:

  • Filter-sterilize final conjugation mixtures with 0.22 μm PVDF/PTFE if necessary; avoid prolonged exposure of proteins to organic co-solvent.
  • Remove excess reagent by desalting columns (e.g., Sephadex G-25), spin filtration (10–30 kDa MWCO), or dialysis, depending on conjugate size.

Item-specific buffer specs (pH range, exact solubility): Not specified for this item; refer to CoA/Spec Sheet.

Green Alternatives

Greenness context (general for SPAAC reagents): DBCO-PEG5-acid enables copper-free click chemistry, eliminating Cu(I) catalysts and associated chelation/remediation. Environmental impact is still influenced by solvent choice and PEGylated organics.

Comparison of strategies (literature/general):

• Copper-free SPAAC (DBCO) vs CuAAC (terminal alkyne + Cu):

  • Pros: avoids copper salts (lower aquatic toxicity), compatible with live systems, fewer purification steps to remove metals.
  • Cons: larger, more complex reagent; synthesis and disposal of PEGylated arylcyclooctynes carry higher embodied energy.

• Alternative cycloalkynes:

  • BCN/DIBAC: sometimes synthesized with fewer steps; slightly slower kinetics may allow finer control; can be more hydrophilic depending on linker.
  • Tetrazine–TCO (iEDDA) as an alternative bioorthogonal pair: extremely fast, often at lower stoichiometry, but tetrazines can be more sensitive to oxidation; choose based on stability and safety profile.

Greener solvent choices for use-phase:

• Favor aqueous buffers with minimal DMSO (≤10%) over neat DMF/NMP when biomolecule stability allows.
• Ethanol or isopropanol can sometimes replace acetonitrile or dichloromethane for small-molecule couplings, though activation efficiency may drop.

Waste minimization and process tips:

• Use high-concentration stocks to reduce solvent volume; apply micro-scale stoichiometry to limit excess reagent.
• Implement solid-supported scavengers to capture unreacted DBCO after conjugation, reducing solvent-intensive purification.
• Evaluate life-cycle impacts: longer PEG chains may improve performance but increase environmental load; select the shortest PEG that meets your application.

Pharmaceutical Uses

Scope: This product is for research use only. The following discusses formulation/manufacturing-relevant aspects without therapeutic claims.

• Role in development workflows:

  • Linker for constructing antibody–drug conjugate (ADC) surrogates, polymer–drug conjugates, or diagnostic probes via SPAAC to azide-bearing payloads or carriers. The carboxylic acid allows installation of DBCO onto amine-containing proteins, peptides, or polymers prior to conjugation to azides.

• Excipient status and compendia:

  • DBCO-PEG5-acid is not a standard pharmacopeial excipient. No USP/EP monograph is typically available for this specific reagent. Any use in GMP settings would require in‑house specification setting, impurity profiling, and stability studies.

• Formulation considerations (general):

  • Solubilization: prepare concentrated stocks in sterile, anhydrous DMSO; dilute into isotonic buffers immediately before conjugation.
  • Residuals: after conjugation, remove unreacted DBCO to limit potential hydrophobic interactions or off-target binding in biological assays.
  • Stability: protect from light and moisture; avoid elevated pH which may affect strained alkyne integrity over time.

• Analytical controls:

  • Characterize conjugation extent by UV-Vis (if payload chromophores are present), LC-MS, or SDS-PAGE with fluorescent azide probes.
  • Establish acceptance criteria for free reagent, aggregate level, and potency (e.g., drug-to-antibody ratio in model systems), as applicable.

Item-specific regulatory status or pharm-grade attributes: Not specified for this item; refer to CoA/Spec Sheet.

Physical Properties

Item-specific physical data from Product Data:

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

Common/literature expectations for DBCO–PEGn–acid analogs (informational, not item specifications):

• Physical state: typically a pale solid or viscous gum at ambient temperature, depending on micro-impurities and hydration.
• Solubility profile: generally soluble in polar aprotic organic solvents (DMSO, DMF, acetonitrile) and alcohols; PEG5 confers partial solubility/miscibility in aqueous buffers when aided by co-solvent (e.g., 5–20% DMSO) and neutralization to the carboxylate; water solubility can vary batch-to-batch.
• Partition behavior: amphiphilic; DBCO core is hydrophobic while PEG chain improves aqueous compatibility (logP not routinely reported; varies with exact substitution, literature values are method-dependent and not universal).
• Optical properties: DBCO has weak absorbance in UV region (aromatic chromophore); PEG and carboxylate do not introduce strong chromophores.
• Melting/boiling points, density, refractive index, pKa: Not specified for this item; refer to CoA/Spec Sheet. For carboxylate pKa, typical aliphatic acids are ~4–5 (literature), but the microenvironment (PEG/aryl proximity) can shift apparent acidity.

Handling notes derived from physical behavior (general guidance):

• Hygroscopicity: PEGylated acids can absorb moisture; maintain desiccation for accurate weighing.
• Viscosity: if semi-solid, warming to ~30 °C can aid dissolution; avoid prolonged heating or light exposure to protect the strained alkyne.

Quality & Grades

Item-specific grade/purity from Product Data:

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

Interpretation and implications (general guidance for this class of reagent):

• Research-grade DBCO-PEG reagents are typically provided at high chemical purity to ensure clean bioconjugation and minimal non-specific labeling. When available, review accompanying CoA for NMR, HPLC, and MS confirmation, and for residual solvent/volatile content.
• UV-Vis/HPLC considerations: For applications in analytical workflows (e.g., conjugate quantitation), low-UV impurities are preferred; HPLC chromatograms in the CoA help assess suitability for sensitive detection.
• Residual metals/specs: Metal content is generally not a primary concern for this class, but if downstream use is metal-sensitive (e.g., enzyme assays), request ICP data if needed.
• Stabilizers: DBCO-PEG5-acid is typically shipped neat without stabilizers. If any stabilizers are present for this specific lot, they will be listed on the CoA and should be considered in downstream reactions.
• Lot-to-lot reproducibility: For conjugation processes, validate coupling efficiency across new lots; monitor by LC-MS where possible.

What to check on the CoA/Spec Sheet for this SKU:

• Exact molecular weight and formula, purity (%), residual solvents, water content (if reported), and recommended analytical ID (e.g., ESI-MS m/z). For any absent parameter: Not specified for this item; refer to CoA/Spec Sheet.

Reaction & Applications

Primary application: copper-free click chemistry (SPAAC) with organic azides.

• SPAAC bioconjugation:

  • DBCO undergoes strain-promoted 1,3-dipolar cycloaddition with azides at ambient temperature, forming stable triazoles without Cu(I) catalysts—ideal for live-cell labeling, protein conjugation, and polymer modification.
  • Kinetics (literature): second-order rate constants commonly ~0.1–1 M−1 s−1 in aqueous media, depending on substitution and conditions; faster than many cyclooctynes, enabling lower reagent excess.
  • Selectivity: orthogonal to most biological functional groups; avoid co-presence of free azides in buffers or preservatives.

• Amide coupling via terminal acid:

  • The –CO2H enables installation onto amine-bearing targets using carbodiimides (EDC, DIC) with NHS or HOBt additives; the resulting DBCO–amide conjugates are then poised for SPAAC downstream.
  • For solid-phase or surface coupling, DMF or NMP with catalytic DMAP can improve rates; control pH 6–7 in aqueous EDC/NHS to preserve DBCO integrity.

• Multipoint ligation strategies:

  • Sequential functionalization: first couple the acid to the scaffold, then perform SPAAC with an azide payload (fluorophore, polymer, drug surrogate) for modular assembly.
  • Orthogonal chemistry: combine with thiol–maleimide or SuFEx reactions on distinct handles for multi-label constructs.

Practical tips:

• Use freshly prepared solutions; avoid prolonged exposure to strong bases which may compromise the strained alkyne.
• For proteins, maintain mild buffer conditions (pH ~7.2) and limit organic co-solvent to protect structure while ensuring reagent delivery.

Reaction Conditions

General conditions (literature; not item specifications):

• SPAAC with azides:

  • Solvent: aqueous buffers (PBS/HEPES, pH 7.0–7.5) with 0–10% DMSO; purely organic media (DMF, MeOH) are also effective for small molecules.
  • Temperature: 20–25 °C (ambient). Reaction remains efficient 4–37 °C; higher temperature modestly accelerates kinetics.
  • Stoichiometry: 1.2–5.0 equivalents of DBCO-PEG5-acid (or its amide) per azide site for complete conversion; lower equivalents possible with longer times.
  • Time: minutes to a few hours depending on concentration (μM–mM range) and matrix; monitor by LC-MS or disappearance of azide IR band (~2100 cm−1).

• Amide coupling (installing DBCO via –CO2H):

  • Organic medium: DCM/DMF (1:1) or neat DMF; EDC (1.1–1.5 eq), NHS (1.1–1.5 eq), base (DIPEA 2–3 eq). 0–25 °C, 0.5–4 h for activation, then add amine; total 2–16 h.
  • Aqueous medium: MES buffer (pH 5.0–6.0) with EDC/NHS for 15–30 min activation; adjust to pH 7.0–7.4 and add amine-bearing target; 0.5–2 h reaction.

• Compatibility notes:

  • Avoid sodium azide in buffers during any step involving free DBCO.
  • Strong bases (>pH 9) or prolonged heating can diminish DBCO reactivity over time.

Expected outcomes (typical literature):

• High chemoselectivity with minimal side products; isolated yields for small-molecule SPAAC often >80%. For biomolecule labeling, substitution levels depend on accessibility and equivalents used.

Safety & Handling

Authoritative safety data must be taken from the SDS for this specific SKU.

Item-specific hazard information from Product Data:

• GHS Classification: Not specified for this item; refer to SDS.
• Signal Word: Not specified for this item; refer to SDS.
• H-Statements: Not specified for this item; refer to SDS.
• Pictograms: Not specified for this item; refer to SDS.

General safety considerations for DBCO-PEG reagents (informational):

• Likely hazards: organic irritant; may cause skin/eye irritation and respiratory irritation. Avoid inhalation of dust/aerosols and contact with skin/eyes.
• Strained alkyne sensitivity: DBCO is stable under normal lab conditions but can be reactive toward azides; keep away from sodium azide and azide-bearing waste unless intentional conjugation is performed.
• Peroxide formation: not typically a concern (no ether solvent), but as an organic compound, store away from strong oxidizers and strong bases/acids that may cause decomposition.
• Light sensitivity: aromatic strained alkynes can slowly degrade under strong light; store protected from light when possible.

PPE and engineering controls (standard best practices):

• Wear lab coat, safety glasses, and appropriate chemically resistant gloves (e.g., nitrile). Handle powders/solutions in a fume hood.

First aid (general):

• Skin/eye contact: rinse with water for several minutes; remove contaminated clothing; seek medical attention if irritation persists.
• Ingestion/inhalation: move to fresh air; rinse mouth; seek medical attention.

Waste: Collect organic waste containing DBCO compounds separately; avoid mixing with azide-containing waste to prevent unintended SPAAC reactions.

Solvent Selection

Polarity and miscibility (general/literature for DBCO–PEG5–acid):

• Polarity profile: amphiphilic; DBCO ring favors organic media, while PEG5 and the acid improve polar/aprotic and mixed aqueous compatibility.
• Typical solvents: DMSO, DMF, acetonitrile, methanol, ethanol. Aqueous buffers are often feasible with 5–20% DMSO or after neutralization to the carboxylate salt; pure water solubility is formulation-dependent.

Choosing solvents by application:

• Direct SPAAC bioconjugation on biomolecules: Use aqueous buffers (PBS, HEPES) with 5–10% DMSO to dissolve the DBCO reagent freshly; maintain biomolecule stability (pH 7.0–7.5). Avoid primary amines if planning EDC/NHS activation in the same step.
• Amide coupling to small molecules/polymers: Use anhydrous DMF or DCM/DMF mixtures with EDC/HOBt or DIC/DMAP; for water-sensitive substrates, rigorously dry solvents and glassware.
• Surface immobilization: For PEGylated surfaces or resins, DMF or NMP often provides optimal wetting and swelling.

Comparison versus alternatives (general):

• DBCO-PEG5-acid vs DBCO-PEG4/PEG12: Shorter PEG lowers aqueous compatibility but increases hydrophobic interactions; longer PEG increases solubility and spacing at the cost of higher MW and potential steric effects.
• DBCO vs BCN/DIBAC: DBCO typically displays faster SPAAC kinetics in water but may be more hydrophobic; solvent choice should balance solubility and biomolecule integrity.

Practical tips:

• Prepare concentrated stock (e.g., 10–50 mM) in dry DMSO; dilute into buffer immediately before use to minimize hydrolysis/aggregation.
• Filter stocks (0.22 μm PTFE) if particulates persist; avoid cellulose filters which may bind hydrophobic moieties.

Storage & Reconstitution

Item-specific conditions from Product Data:

• Storage Conditions: Store at -20°C.
• Shipped In: Ice chest + Ice pads.
• Research Use Note: For research use only.

General best practices for this class of reagent (supplemental guidance; not a substitute for CoA/SDS):

• Light/moisture protection: Store in amber, tightly sealed containers under desiccation (drying agent) to limit hydrolysis and potential photodegradation of the strained alkyne.
• Freeze–thaw: Minimize cycles. If supplied as a solid or semi-solid, consider aliquoting upon first opening. If supplied in solution, subdivide into single-use aliquots and store at -20 °C.
• Reconstitution:
  • For stock solutions, dissolve in anhydrous DMSO or DMF to 10–50 mM. Warm gently (≤30 °C) and vortex/sonicate if needed. Filter through 0.22 μm PTFE if particulates remain.
  • For aqueous use, dilute the organic stock into buffer immediately before use. If necessary, adjust pH to 7.0–7.5 and keep final DMSO ≤10% for protein compatibility.
• Stability after reconstitution (literature/general): Stocks in dry DMSO at -20 °C are commonly stable for weeks to a few months when protected from light; prepare fresh working solutions on the day of use.
• Incompatibilities: Avoid storing or handling with azide-containing reagents/preservatives; prevent exposure to strong bases or oxidants.

Always consult the lot-specific CoA/SDS for definitive handling and stability information for SKU D596732.

Structure & Identity

Brief description: DBCO-PEG5-acid is a strained-alkyne bioconjugation handle consisting of a dibenzocyclooctyne (DBCO) core tethered via a short polyethylene glycol spacer (PEG5, five ethylene glycol units) to a terminal carboxylic acid.

• SKU: D596732
• Product Name: DBCO-PEG5-acid
• Category: Chemical and Biochemical Reagents (research use only)

Item-specific identifiers from Product Data:

• 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/literature description):

• Core functionality: a dibenzocyclooctyne ring system (a strained cyclooctyne fused to two benzene rings) that undergoes fast strain‑promoted azide–alkyne cycloaddition (SPAAC) without copper catalysts.
• Linker: approximately five –CH2–CH2–O– repeats (PEG5) providing hydrophilicity, flexibility, and spacing from surfaces/biomolecules.
• Terminal handle: a free carboxylic acid (–CO2H) for amide coupling to primary amines (e.g., via EDC/NHS chemistry) or for activation to NHS esters.
• 2D structure (descriptive): two aromatic rings flank a distorted 8‑membered alkyne-containing ring; one benzylic position bears an ether-linked PEG chain terminating in –CO2H.

Stereochemistry and isomerism (general):

• DBCO possesses ring strain but no stereogenic centers in the alkyne core; PEG linker is achiral; overall molecule is typically a single constitutional isomer with rotamers around ether bonds.

Synthetic Utility

Functional group portfolio and reactivity (general for DBCO-PEG5-acid):

• Strained alkyne (DBCO): engages azides rapidly via SPAAC to form 1,2,3-triazoles; orthogonal to thiols, alcohols, and most amines under neutral conditions.
• Carboxylic acid terminus: compatible with carbodiimide-mediated coupling (EDC, DIC) to make amides; convertible to active esters (NHS, TFP) for streamlined bioconjugation.
• PEG linker: enhances solubility, reduces non-specific adsorption, and provides spacing to mitigate steric hindrance.

Retrosynthetic value:

• Introduces a versatile “click handle” onto complex scaffolds late in synthesis, minimizing protecting-group gymnastics. The acid can be coupled under mild conditions to sensitive substrates (peptides, polymers, nanoparticles), creating modular routes to libraries of conjugates via subsequent SPAAC with azide-bearing tags.

Complementary/orthogonal strategies:

• Combine with alkene–tetrazine iEDDA, thiol–maleimide, or SuFEx to assemble multi-functional constructs on distinct handles.
• Convert the acid to an NHS ester in situ for rapid labeling of lysines on proteins; quench residual NHS with Tris or ethanolamine after coupling.

Downstream processing tips:

• Purify small-molecule conjugates by RP-HPLC; PEGylated species elute late—use shallow gradients and volatile buffers (e.g., ammonium acetate) for MS compatibility.
• For polymer/nanoparticle surfaces, extensive washing or ultrafiltration removes excess reagent; assess loading by azide consumption (e.g., azide-IR band at ~2100 cm−1 disappearance, literature) or by reacting a tracer azide dye.

Target Specificity

Not applicable for this chemical reagent. DBCO-PEG5-acid is not an antibody, enzyme, or affinity reagent with biological target specificity. It is a general-purpose bioorthogonal coupling handle that reacts with organic azides regardless of biological origin.

Any target/clone/isotype information: Not specified for this item; not applicable.