DBCO-PEG1-NH-Boc - ≥98%

Cat. No.: D597159

GRADE & PURITY ≥98%

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Application

Antibody Drug Conjugates(ADC), Drug Delivery, Surface Modification, PEGylation of Protein, Peptide & Oligo

Overview

DBCO-PEG1-NH-Boc is a PEG derivative with a DBCO group and a Boc-protected amine. The DBCO can undergo copper-free Click Chemistry reactions with azides. The Boc protecting group can be removed under acidic conditions to further react.

Specifications

Specifications & Purity

≥98%

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

≥98%

Chemical and Physical Properties

• Solubility: Solubility in DMSO, DCM, DMF

Application Protocols

Illustrative protocols for research use (general guidance; optimize for your system). These are not item‑specific specifications.

A. SPAAC labeling of an azide‑modified protein

• Prepare a 10–50 mM stock of DBCO-PEG1-NH-Boc in anhydrous DMSO.
• Buffer the protein at 1–10 mg/mL in PBS or HEPES, pH 7.2–7.6. Optional: include 5–10% DMSO to aid solubility.
• Add 3–10 molar equivalents of DBCO stock per protein‑azide site while gently mixing; keep final DMSO ≤10%.
• Incubate 1–4 h at room temperature (or 4–16 h at 4–8°C). Monitor by LC–MS or SDS‑PAGE (if a chromophore will be added later, mass shift is preferred).
• Remove excess reagent by size‑exclusion or desalting. Analyze by LC–MS to confirm triazole formation.

B. Boc deprotection on the conjugate (if amine is required)

• Exchange into organic‑tolerant solvent (e.g., add ACN) or precipitate/re‑dissolve as appropriate for the biomolecule.
• Treat with 20–50% TFA in DCM (small molecules) or compatible acid conditions for bioconjugates (brief, chilled, and immediately neutralized). Monitor by MS.
• Neutralize, desalt, and reformulate into the desired buffer.

C. Small‑molecule azide coupling

• Dissolve both partners (1–10 mM) in ACN/DMSO. Add 1.1–2.0 equiv DBCO reagent.
• Stir at RT for 0.5–2 h; monitor by LC–MS.
• Purify by flash or prep HPLC.

Note: Adjust stoichiometry, time, and solvent according to substrate accessibility and solubility.

Biological Roles

This compound does not possess an inherent biological role; it is a synthetic linker used to create defined bioconjugates through bioorthogonal chemistry.

General context (literature):

• Bioorthogonal SPAAC: DBCO reacts selectively with azide groups that are absent in native biomacromolecules, enabling site‑selective labeling of proteins, glycans, nucleic acids, and lipids introduced via metabolic or chemical methods.
• Cell and tissue labeling: Because SPAAC is copper‑free, it is compatible with live‑cell environments at low micromolar reagent concentrations, minimizing perturbation compared to CuAAC. Short PEG spacers can balance membrane permeability and aqueous behavior.
• Post‑conjugation versatility: Following SPAAC, Boc deprotection generates a primary amine on the conjugate, serving as a handle to attach functional payloads (fluorophores, affinity tags, polymers) or to modulate charge/hydrophilicity.

Considerations:

• Permeability vs. specificity: The hydrophobic DBCO core may enhance cell membrane interaction; control experiments and time‑course studies help optimize labeling conditions and limit nonspecific binding.
• Protein compatibility: SPAAC proceeds under near‑physiological pH and ionic strength. Maintain low organic co‑solvent levels to preserve protein structure.

Note: All uses are for research applications only. No medical or clinical use is intended or implied.

Buffer Applications

This reagent is not a buffering agent. However, buffer choice critically influences solubility and performance in SPAAC bioconjugations.

General guidance (not item-specific specifications):

• Reaction buffers: PBS (pH 7.2–7.6), HEPES (pH 7.0–8.0), or Tris (note: Tris has a primary amine; acceptable for SPAAC but may interfere with subsequent NHS‑ester couplings after Boc deprotection—prefer phosphate/HEPES if planning amide coupling next).
• Co‑solvents: 2–20% v/v DMSO or DMF can be used to maintain reagent solubility; minimize organic content for live‑cell work (≤1–2% when possible).
• Ionic strength: physiological salt (100–150 mM NaCl) is generally compatible and can reduce nonspecific biomolecular interactions.
• pH considerations: SPAAC is broadly tolerant (pH ~6–8.5). If Boc deprotection is performed post‑click, carry it out in organic solvent with acid or in carefully controlled aqueous acid, followed by rapid neutralization and buffer exchange.

Practical tips:

• Filter buffers (0.22 µm) and degas if performing sensitive analytics post‑reaction.
• For protein conjugations, add the DBCO reagent last from a concentrated stock to minimize precipitation; gentle mixing at 4–25°C is typical.
• For surface labeling, rinse extensively with buffer containing a small percentage of detergent (e.g., 0.01% Tween‑20) to minimize nonspecific adsorption, if compatible with the system.

Green Alternatives

Considerations in choosing DBCO‑based SPAAC relative to alternatives center on catalyst requirements, solvent choices, and waste minimization.

Comparison of azide–alkyne strategies (general literature perspective):

• DBCO‑SPAAC (this reagent):

  • Pros: copper‑free (no metal catalyst, lower cytotoxicity and metal waste), proceeds in water/biological media, simple workflow.
  • Cons: DBCO synthesis has a higher upstream footprint; hydrophobic core may require organic co‑solvent; potential off‑target reactions with highly nucleophilic thiols at high concentrations are rare but reported.

• CuAAC (terminal alkyne + Cu(I) catalyst):

  • Pros: fast kinetics with suitable ligands; inexpensive alkynes; wide substrate scope.
  • Cons: requires copper and often stabilizing ligands; copper removal from biomolecules generates additional waste and may compromise activity.

• BCN (bicyclononyne) or DIFO cyclooctynes:

  • Pros: different reactivity/solubility profiles; sometimes improved aqueous handling.
  • Cons: similar synthetic complexity; may show different selectivity/kinetics; availability and cost vary.

Greener practice tips (applicable generally):

• Use aqueous buffers with minimal DMSO/DMF (≤10% where feasible) while maintaining solubility.
• Employ room‑temperature reactions to reduce energy input.
• Purify by aqueous SEC/desalting rather than extensive organic chromatography when working with biomolecules.
• Prepare concentrated stocks to minimize solvent volumes and container waste; aliquot to reduce freeze–thaw cycles.

Pharmaceutical Uses

DBCO-PEG1-NH-Boc is supplied for research use only. It is not an active pharmaceutical ingredient nor an approved excipient. Nevertheless, similar linkers are widely evaluated in pharmaceutical research and manufacturing development.

Context in development (general literature):

• Bioconjugate manufacturing R&D: Copper‑free SPAAC is used to prepare antibody–drug conjugates (ADCs), protein–polymer conjugates, nanoparticle functionalization, and targeted delivery systems using azide handles introduced via chemical or enzymatic methods.
• Process considerations: Avoidance of copper simplifies downstream purification and reduces risk of metal‑catalyzed oxidation of proteins or peptides. Short PEG spacers can modulate hydrodynamics, DAR distribution (for ADCs), and stability.
• Post‑click derivatization: Boc deprotection affords a primary amine for installing payloads via amide formation, enabling modular assembly of multi‑functional constructs.

Caveats:

• No pharmacopeial monograph is associated with this material (general statement); specification setting is project‑specific.
• For GMP‑adjacent studies, define impurity profiles (residual solvents, related substances), and implement orthogonal analytics (HPLC, LC–MS, NMR) and metal testing if required by process history.

Statement: This product is for laboratory research use only and is not intended for diagnostic, therapeutic, or human/animal use.

Physical Properties

Item-specific physicochemical specifications are not provided in the current listing. Where helpful, general/literature guidance for DBCO–PEG–Boc motifs is summarized below (not specifications for this item).

Item-specific (this SKU):

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Melting point, boiling point, density, refractive index: Not specified for this item; refer to CoA/Spec Sheet.
• Solubility (spec): Not specified for this item; refer to CoA/Spec Sheet.

General/literature characteristics for analogous DBCO-PEGn-Boc reagents (indicative only):

• Physical state: typically off‑white to light tan solid; amorphous or low‑melting.
• Solubility: good in polar aprotic organic solvents (DMSO, DMF, NMP, acetonitrile); soluble in chlorinated solvents (DCM, chloroform); variably soluble in alcohols (MeOH, EtOH); limited aqueous solubility unless co‑solvent or surfactant is used.
• Partitioning: overall amphiphilic due to PEG/urethane, but the polycyclic DBCO increases hydrophobicity; aqueous logP not typically reported.
• Acid/base: Boc carbamate is acid‑labile; the protected amine is non‑basic. After deprotection, the primary amine is basic (pKa of alkyl ammonium typically ~9–10, literature), improving aqueous solubility under mildly acidic conditions.

Practical notes (general):

• Prepare concentrated stocks in anhydrous DMSO or DMF, then dilute into the reaction/buffer just before use to avoid adventitious hydrolysis.
• Protect from strong acids if Boc retention is required; avoid prolonged exposure to aqueous base which may hydrolyze carbamates slowly.

Quality & Grades

Item-specific grade/purity is not provided in this listing.

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

General guidance on quality expectations for bioconjugation linkers:

• Research grade: suitable for synthetic and labeling workflows; typical acceptance criteria focus on chemical purity (HPLC/LC–MS), identity (NMR/MS), and residual solvent/moisture controls. When UV detection is used, low baseline drift is desirable but not guaranteed unless stated (e.g., HPLC grade solvent attributes are irrelevant here).
• Metal content: Not specified for this item; refer to CoA/Spec Sheet. For sensitive biological applications, low residual transition metals are often preferred; request elemental data if needed.
• Stabilizers: Not specified for this item; refer to CoA/Spec Sheet. DBCO reagents usually do not require added stabilizers; they should be kept dry and cool.
• What the Boc means: The tert‑butyl carbamate protects the primary amine during SPAAC, preventing undesired side reactions with activated esters. After click, acid deprotection reveals a free amine for secondary conjugation steps.

Recommendations:

• For quantitative bioconjugations, request or verify lot‑specific purity and water content on the CoA.
• Run a small‑scale pilot conjugation and analyze by LC–MS to benchmark conversion and detect potential side products (e.g., partial hydrolysis).

Reaction & Applications

This reagent is designed for copper‑free bioorthogonal conjugation via the DBCO alkyne and staged unveiling of a primary amine after Boc removal.

Key reaction families (general/literature):

• SPAAC (Strain‑Promoted Azide–Alkyne Cycloaddition): rapid, catalyst‑free cycloaddition with organic or biomolecular azides to form stable triazoles. Compatible with live cells and delicate proteins due to the absence of Cu(I).
• Boc deprotection: acidolysis (e.g., TFA or HCl in suitable solvents) to reveal a primary amine for subsequent amide/urea/thiourea formation.
• Secondary ligations post‑deprotection: NHS ester coupling to carboxylates; isocyanate/chloroformate reactions; reductive amination with aldehydes; coupling via carbodiimides (EDC/HOBt) or uronium reagents (HATU, TBTU) when the counterpart provides a carboxyl group.

Application scenarios:

• Two‑stage bioconjugation: (1) SPAAC to install the DBCO payload onto azide‑modified biomolecules, (2) Boc deprotect to generate a handle for further functionalization (e.g., dye, drug, polymer).
• Surface chemistry: immobilization on azide‑functional surfaces, then amine derivatization to introduce capture ligands.
• Polymer/material modification: click to azide‑bearing polymers, then amine coupling to tune hydrophilicity or add crosslinkers.

Practical tips:

• Maintain anhydrous, oxygen‑free conditions for long stock stability; SPAAC itself tolerates air and water.
• Use slight excess (1.1–2.0 equiv) of DBCO reagent for small‑molecule azides; for biomolecules, 3–10 molar equivalents per azide site are common (optimize by LC–MS).
• Post‑click cleanup: remove excess reagent by SEC or spin desalting; confirm triazole formation by MS.

Reaction Conditions

The following are general literature/practice guidelines for analogous DBCO‑PEGn‑Boc reagents; they are not specifications for this item.

SPAAC with azides:

• Solvent/buffer: aqueous buffers (PBS, HEPES) with 2–20% DMSO or DMF co‑solvent to solubilize the DBCO reagent; purely organic media (ACN, DMSO, DMF, DCM) for small molecules.
• Concentration: biomolecule labeling 5–100 µM in macromolecule; DBCO typically 3–10 molar equivalents per azide site. Small‑molecule reactions often 1–50 mM.
• Temperature: 20–25°C (room temperature) is common; lower temperatures (4–10°C) slow kinetics but may preserve protein activity; mild warming (30–37°C) can accelerate reaction in vitro.
• Time: minutes to a few hours for small molecules; 1–24 h for biomolecules depending on azide accessibility and concentration.
• Atmosphere: ambient; oxygen exclusion not required.

Boc deprotection (post‑click when desired):

• Reagents: TFA in DCM or neat TFA; alternative mineral acids (e.g., HCl in dioxane) can be used where compatible.
• Conditions: 20–50% TFA in DCM, 0.5–2 h at RT for many Boc carbamates (literature). Monitor by LC–MS. Quench by solvent evaporation and basification or by immediate neutralization, then purify.
• Aqueous options: dilute HCl at low temperature for acid‑tolerant substrates; promptly neutralize and desalt.

Post‑reaction workup:

• Biomolecules: remove excess small molecules by SEC (e.g., Sephadex G‑25) or spin columns; confirm by UV/Vis (if chromophore attached) and LC–MS.
• Small molecules: concentrate and purify by flash chromatography or preparative HPLC as appropriate.

Safety & Handling

Authoritative safety data must be taken from the product’s SDS. The following are general precautions for DBCO- and Boc-containing linkers; they are not item-specific classifications.

Item-specific hazard data:

• Signal word: Not specified for this item; refer to SDS.
• GHS classification/pictograms: Not specified for this item; refer to SDS.
• H-statements: Not specified for this item; refer to SDS.

General handling guidance (for similar materials):

• Likely hazards: organic solid/liquid that may cause skin/eye irritation; harmful if swallowed or inhaled. DBCO moieties can be reactive toward azides; keep away from potentially energetic inorganic azides.
• PPE: lab coat, safety glasses or face shield, and appropriate chemically resistant gloves (e.g., nitrile). Use in a fume hood to avoid inhalation of vapors/aerosols.
• Incompatibilities: strong acids (Boc cleavage), strong bases (carbamate hydrolysis over time), powerful oxidants, and reactive azide salts. For bioconjugation, azide‑functional biomolecules are compatible; avoid metal azides or hydrazoic acid conditions.
• First aid (overview):
  • Skin/eye contact: rinse with water for ≥15 minutes; remove contaminated clothing; seek medical attention if irritation persists.
  • Inhalation: move to fresh air; seek medical advice if symptoms occur.
  • Ingestion: rinse mouth; do not induce vomiting; seek medical care.
• Special risks: moisture and acid sensitivity of the Boc group; protect from prolonged light and heat to minimize degradation of strained alkynes.
• Waste: collect organic waste according to institutional/municipal regulations; segregate from oxidizers and azide salts.

Solvent Selection

DBCO-PEG1-NH-Boc combines a hydrophobic strained alkyne with a short PEG and a Boc carbamate, yielding good solubility in polar aprotic media and limited aqueous compatibility.

General solvent guidance (literature/practice; not item-specific specifications):

• Preferred stock solvents: anhydrous DMSO or DMF (high solubility, good stability of Boc group under neutral conditions).
• Processing solvents: acetonitrile, NMP; chlorinated solvents (DCM, CHCl3) if water exclusion is required.
• Aqueous use: dilute organic stocks into buffered media immediately before use (e.g., PBS, HEPES) with 5–30% DMSO or DMF as co‑solvent to maintain solubility during SPAAC.
• Avoid: strong acids (risk of Boc loss) unless intentional deprotection; prolonged exposure to strong base; highly nucleophilic alcohols in the presence of activating agents that could transcarbamoylate.

Selection tips:

• For live‑cell labeling, DMSO stocks diluted into serum‑free media to ≤1–2% v/v DMSO are common to balance solubility and cell compatibility (general guidance).
• For protein conjugations in PBS, maintain a small percentage of DMSO/DMF to prevent precipitation; gently tumble instead of vigorous vortexing to minimize foaming/aggregation.

Brief comparison (general):

• DMSO: highest solvency and biocompatibility at low %; hygroscopic—use dry stocks.
• DMF: excellent solvency; residual DMF may interfere with downstream lyophilization; ensure thorough removal.
• ACN: useful for RP-HPLC co‑elution; lower solvency for some DBCO reagents; mixes well with water.

Storage & Reconstitution

Item-specific storage/shipping:

• Storage conditions: Store at −20°C (per product data).
• Shipped in: Ice chest + ice pads (per product data).
• Research use: For research use only.

General handling and reconstitution guidance for DBCO‑PEG‑Boc reagents:

• Protect from moisture and light. Use desiccant in a tightly sealed container. Allow vials to warm to room temperature in a desiccator before opening to prevent condensation.
• Prepare concentrated stocks (e.g., 10–50 mM) in anhydrous DMSO or DMF. Filter (0.2 µm PTFE) if particulates are present.
• Aliquot single‑use volumes and store at −20°C. Minimize freeze–thaw cycles to preserve integrity.
• Aqueous working solutions should be prepared immediately before use; prolonged storage in water or acidic media risks Boc cleavage or hydrolysis.
• Stability/shelf life: Not specified for this item; refer to CoA/Spec Sheet. As a general practice, periodically check stock solutions by LC–MS for degradation (e.g., hydrolysis or side reactions).

Disposal and cleanup:

• Rinse glassware with suitable organic solvent (DMSO/DMF/ACN, then IPA) before aqueous washes. Collect organic waste according to institutional guidelines.

Note: If Boc deprotection is intended, perform on a small test portion first to establish conditions compatible with your substrate.

Structure & Identity

A strained-alkyne bioconjugation handle featuring a short PEG spacer and a Boc-protected amine for orthogonal, two-stage coupling workflows.

• Product name: DBCO-PEG1-NH-Boc (dibenzocyclooctyne–PEG1–tert‑butyl carbamate)
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
• CAS: 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.

Structural features (general description):

• DBCO core: a dibenzocyclooctyne (two benzene rings fused to a cyclooctyne) bearing a highly strained internal alkyne that undergoes rapid strain‑promoted azide–alkyne cycloaddition (SPAAC) without copper.
• PEG1 spacer: a single ethylene glycol unit (–O–CH2–CH2–O–) that improves solubility and provides minimal spatial separation between the DBCO and the terminal functionality.
• Terminal functionality: Boc‑protected primary amine (–NH–Boc), i.e., a tert‑butyl carbamate that masks a nucleophilic amine for stability and orthogonality; deprotected under acidic conditions to unveil –NH2 for further conjugation.
• 2D description in words: an aromatic–alicyclic polycyclic framework bearing an internal C≡C within an eight‑membered ring, tethered via a short PEG ether linkage to a carbamate with a tert‑butyl substituent.

Notes:

• No stereocenters are expected in the typical DBCO-PEG1-NH-Boc scaffold.
• Exact regiochemistry and substituent positions can vary by supplier; consult the CoA/SDS for definitive structure.

Synthetic Utility

Functional group ensemble and their synthetic leverage (general):

• Strained alkyne (DBCO): enables catalyst‑free cycloadditions with organic/biomolecular azides (SPAAC), forming robust 1,2,3‑triazoles under mild conditions.
• Boc‑protected amine: orthogonal to SPAAC; removable under acid to reveal a primary amine for diverse bond constructions (amides, ureas, carbamates, sulfonamides).
• PEG1 ether: improves solubility and spacing; can attenuate steric crowding around the reactive center.

Typical transformations:

• Click‑then‑decorate: Perform SPAAC onto an azide‑tagged scaffold (small molecule, polymer, biomolecule). After purification, deprotect Boc and couple the emergent amine to carboxylic acids (EDC/HOBt, HATU) or NHS esters.
• Protecting‑group choreography: If an amine‑reactive partner is present pre‑click, Boc ensures chemoselectivity until click completion.
• Solid‑support/surface modification: Immobilize via azide termini on resins/surfaces, then amine‑mediated attachment of capture ligands or reporters.

Retrosynthetic value:

• The reagent effectively condenses multiple operations (installation of click handle + latent amine) into a single building block, simplifying route scouting for modular conjugates.

Practical insights:

• Maintain neutral to slightly basic conditions during SPAAC if labile functionalities are present elsewhere; perform Boc removal last unless subsequent steps demand the free amine.
• For analytics, LC–MS readily detects mass increases consistent with triazole formation; after deprotection, expect a −101 Da change relative to Boc loss (literature) on the relevant fragment.

Target Specificity

Not applicable. This product is a small‑molecule linker, not a biological affinity reagent or antibody. It does not have intrinsic target specificity beyond the chemical selectivity of SPAAC for azides.