LCL-PEG3-N3 , CAS No.3033849-90-7

CAS: 3033849-90-7 Cat. No.: L1448731 Formula: C₃₂H₄₅N₇O₆S Molecular Weight: 655.81

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

LCL-PEG3-N3 is a decoy oligonucleotide ligand for E3 ligase which can be used for developing chimeric molecules LCL-ER(dec), degrading the estrogen receptor. LCL-PEG3-N3 is a click chemistry reagent, it contains an Azide group and can undergo copper-catalyzed azide-alkyne cycloaddition reaction (CuAAc) with molecules containing Alkyne groups. It can also undergo strain-promoted alkyne-azide cycloaddition (SPAAC) reactions with molecules containing DBCO or BCN groups.

Specifications

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.

Names and Identifiers

Molecular Weight

655.81

Application Protocols

No item-specific tested application protocols are provided in the Product Data. The following are general, literature-based examples for PEG–azide click chemistry. Adjust to your system and verify on small scale.

Example 1: CuAAC small-molecule conjugation

• Dissolve LCL-PEG3-N3 and an alkyne partner each at 10 mM in 1:1 H2O/t-BuOH.
• Add CuSO4 (1 mol%) and THPTA (5 mol%) relative to limiting reagent; start stirring.
• Add sodium ascorbate (5–10 mol% vs substrate). React at RT for 2–4 h.
• Quench with EDTA, extract or purify by preparative HPLC. Verify disappearance of azide IR band (~2100 cm−1, literature).

Example 2: SPAAC bioconjugation

• Prepare solutions of the azide reagent and DBCO-labeled partner (50–100 µM) in PBS with 5–10% DMSO if needed.
• Mix at 1:1 to 1:1.5 stoichiometry (DBCO in slight excess) and incubate at 25–37°C for 1–3 h.
• Desalt (spin column) or dialyze to remove excess small molecules.

Notes

• Buffer components (e.g., Tris) may chelate copper; for CuAAC prefer HEPES/PBS and include stabilizing ligands.
• For sensitive “LCL” motifs (if photolabile), minimize light exposure during setup and purification. Item-specific constraints should be confirmed on the CoA/Spec Sheet.

Biological Roles

Item-specific biological roles are not provided in the Product Data.

General context for PEG–azide linkers (literature)

• Bioorthogonality: Azide functionality is minimally reactive toward native biological nucleophiles, enabling selective ligation in complex matrices when paired with alkynes (CuAAC) or strained alkynes (SPAAC).
• PEG effects: Short PEG spacers like PEG3 increase hydrophilicity, can reduce protein adsorption, and modulate linker flexibility. They often improve aqueous compatibility of conjugates without excessively increasing size.
• Applications in chemical biology: Installation of affinity tags, fluorophores, and handles for pull-down or imaging after metabolic labeling (e.g., azide-bearing glycans) of biomolecules; the azide here would typically be the counterpart in the ligation.
• Enzymatic interactions: PEG linkers are generally inert to most enzymes, although highly hydrophilic segments can influence cellular uptake and distribution in cell-based experiments.

Caveats

• Copper used in CuAAC can be cytotoxic; for live-cell contexts, SPAAC is preferred. For this product, no suitability for live-cell use is claimed; it is for research use only.
• Always confirm endotoxin/bioburden requirements if planning biological exposure; such specifications are not provided for this item.

Buffer Applications

This item is not a buffer reagent per se. However, PEG–azide ligations are commonly conducted in buffered aqueous media. The following are general, literature-based considerations (not item-specific):

• Common buffers for CuAAC: PBS (pH 7.2–7.4), HEPES (pH 7.2–7.5), or Tris (note: Tris can coordinate copper and may inhibit; HEPES/PBS often preferred). Maintain 10–100 mM buffer strength.
• Additives: Sodium ascorbate (reducing agent for CuSO4), and Cu-ligands such as THPTA or BTTAA to stabilize Cu(I) and protect biomolecules.
• Solvent cosolvents: 5–30% t-BuOH, ethanol, or DMSO can help solubilize hydrophobic partners while preserving protein integrity in bioconjugations.
• Degassing: For sensitive substrates, gentle argon sparging can reduce oxidative side reactions mediated by copper/oxygen.
• SPAAC conditions: Often performed in pure buffers without copper; choose buffer to maintain biomolecule stability and ionic strength.

Practical recipes (illustrative)

• CuAAC stock system: 10 mM CuSO4, 50 mM THPTA in water; 100 mM sodium ascorbate prepared fresh. Mix with substrates in PBS to achieve 50–200 µM Cu, 0.5–2 mM ligand, and 1–10 mM ascorbate, adjusting per substrate reactivity.

Note: Exact conditions and compatibility must be optimized for your conjugation partners; refer to the CoA/Spec Sheet for any item-specific constraints.

Green Alternatives

Context

• Click-chemistry workflows often default to DMF, DCM, or acetonitrile. Greener choices can reduce hazard and waste without sacrificing performance.

Greener solvent/system options (literature)

• Water or water-rich media: CuAAC proceeds efficiently in H2O/t-BuOH or H2O/EtOH mixtures with appropriate ligands; maximizes safety and ease of workup.
• 2-Methyltetrahydrofuran (2-MeTHF): Bio-based alternative to THF/Et2O for extractions and some conjugations; good phase behavior and lower peroxide tendency than ethers like THF.
• Ethyl acetate and acetone: Preferable to chlorinated solvents for workups and intermediate purifications.
• Propylene carbonate: High-permittivity, low-volatility solvent as a safer replacement for DMF in some coupling steps; consider viscosity and workup strategy.

Comparison highlights (general)

• t-BuOH/H2O vs DMF: Similar or better CuAAC rates in many systems; t-BuOH/H2O eases removal and reduces worker exposure.
• 2-MeTHF vs DCM: Reduces chlorinated waste; suitable for extractions and some silica chromatography blends.

Operational tips

• Use copper-stabilizing ligands (e.g., THPTA) to enable high aqueous content reactions.
• For SPAAC, purely aqueous conditions are often viable; PEG3 enhances solubility of the azide partner, reducing need for high-boiling polar aprotics.

Note

• Select the green alternative based on your other coupling partner’s solubility and stability. Validate on small scale before scale-up.

Pharmaceutical Uses

No pharmacopeial status or excipient role is provided for this item.

General R&D context (non-clinical)

• Conjugation handle: PEG–azide linkers are used in discovery-stage bioconjugation to attach small molecules, affinity tags, or payloads to alkyne-bearing scaffolds, aiding SAR exploration and targeted delivery constructs.
• Solubility tuning: Short PEG spacers can improve formulation behavior of screening compounds and conjugates in assay buffers.
• Surface modification: Installation of azide groups on polymers or nanoparticles to enable subsequent click functionalization during formulation development.

Manufacturing/process considerations (research scale)

• Residual copper removal (if CuAAC is used) via chelating resins (e.g., QuadraPure TU, EDTA washes) or scavengers is standard to meet internal specifications in process research.
• Analytical controls: LC–MS and ICP–MS (for copper) are typically employed to qualify intermediates; release specs should be defined internally as this product does not list pharmacopeial compliance.

Disclaimer

• For research use only. Not for human or veterinary use, drug substance, or clinical applications. No therapeutic claims are made or implied.

Physical Properties

Item-specific values

• Boiling point: Not specified for this item; refer to CoA/Spec Sheet.
• Melting point: Not specified for this item; refer to CoA/Spec Sheet.
• Density: Not specified for this item; refer to CoA/Spec Sheet.
• Refractive index: Not specified for this item; refer to CoA/Spec Sheet.
• Solubility: Not specified for this item; refer to CoA/Spec Sheet.
• LogP, pKa: Not specified for this item; refer to CoA/Spec Sheet.

General/literature expectations for PEG3–azide linkers (informational only)

• Physical state: Typically low-melting solids, waxy solids, or viscous oils depending on the attached core.
• Polarity/solubility: PEG3 segments confer significant polarity and hydrogen-bond acceptance; such compounds are usually soluble in polar aprotic solvents (DMSO, DMF, acetonitrile) and often miscible or sparingly soluble in water depending on the non-PEG portion.
• Volatility: Low, owing to PEG content; vacuum drying is typically feasible at mild temperatures.
• Hygroscopicity: PEG-containing molecules can be hygroscopic; handling under dry conditions helps maintain integrity and accurate weighing.

Practical characterization tips (general)

• NMR: PEG repeats give characteristic broadened multiplets near 3.3–3.8 ppm (1H) and signals around 70 ppm (13C); the azidomethyl region (if present) often appears near 3.2–3.5 ppm.
• IR: Organic azide exhibits a distinct asymmetric stretch near 2090–2120 cm−1 (literature), and C–O–C stretches for PEG near 1100 cm−1.
• MS: Diagnostic +42.0 Da for azide-to-triazole mass shift upon click reaction; confirm exact mass from the CoA/Spec Sheet.

Quality & Grades

Item-specific grade/purity

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

How to interpret grades (general guidance)

• Research grade: Suitable for most synthetic and screening workflows; trace impurities may be present. Check chromatography suitability if using in analytical contexts.
• Purity reporting: For linker-reagents, purity is often reported by HPLC/UPLC area percent and/or NMR integration. If your application is surface conjugation or medicinal chemistry SAR, request the CoA with residual solvent, water content (Karl Fischer), and volatile impurities.
• Stabilizers: None are listed for this item. If stabilizers are present in other lots of similar reagents, they can influence downstream reactions (e.g., UV-sensitive groups or inhibitors). Always review the CoA/Spec Sheet.

Recommended quality checks before use (general)

• Verify identity by NMR/HRMS against the structure on the CoA/Spec Sheet.
• Run a quick HPLC to assess purity and look for low-level PEG oligomers or hydrolysis products.
• For bioorthogonal use, confirm azide integrity by a small-scale CuAAC test-click with a standard alkyne probe and analyze conversion.

Documentation

• For definitive specifications and acceptance criteria, refer to the lot-specific CoA/Spec Sheet and SDS.

Reaction & Applications

Manufacturer applications

• Not specified in Product Data.

General/literature applications for PEG–azide linkers

• Bioorthogonal ligation: Terminal azide enables copper-catalyzed azide–alkyne cycloaddition (CuAAC) with terminal or internal alkynes to form 1,4-disubstituted triazoles. Useful for probe tagging, surface modification, and polymer functionalization.
• Copper-free click: Reacts with strained alkynes (e.g., DBCO, BCN, BARAC) via SPAAC for metal-free conjugations, advantageous with sensitive biomolecules.
• Solubility modulation: PEG3 spacer increases aqueous compatibility, can reduce nonspecific adsorption, and provides spatial separation between a core scaffold and the installed functionality.
• Staudinger ligation/traceless variants: Azide can undergo phosphine-mediated ligation to yield amide linkages under mild conditions (literature), though less common than CuAAC.
• Reductive transformations: Azide reduction to primary amine (e.g., Staudinger reduction or catalytic hydrogenation) for subsequent amide coupling or urea formation.

Practical tips

• For CuAAC, employ CuSO4/sodium ascorbate with a stabilizing ligand (e.g., THPTA or TBTA) to suppress copper-induced side reactions and improve rate in aqueous media.
• Maintain anhydrous conditions for moisture-sensitive counterparts; PEG segments can carry adventitious water—pre-dry solvents and consider azeotropic drying of reagents.
• If the “LCL” core is photolabile in your formulation, minimize light exposure during synthesis; verify on the CoA/Spec Sheet.

Reaction Conditions

The Product Data do not specify conditions. The following are literature-based, general guidelines for azide–alkyne ligations and related steps:

CuAAC (copper-catalyzed click)

• Solvent: H2O/t-BuOH (1:1), H2O/EtOH, DMSO/H2O, or DMF/H2O.
• Catalyst system: 0.5–5 mol% CuSO4 with 1–2 equiv sodium ascorbate relative to Cu, plus 2–10 mol% of a ligand such as THPTA, BTTAA, or TBTA.
• Concentration: 1–10 mM of each coupling partner is typical for small molecules; higher dilution can reduce oligomerization on surfaces.
• Temperature/time: 20–40°C, 0.5–16 h depending on substrate; agitation improves mass transfer.
• Workup: Aqueous EDTA wash to remove copper, followed by extraction or desalting.

SPAAC (copper-free click)

• Solvent: Aqueous buffers (PBS, HEPES) or mixtures with 5–20% DMSO.
• Stoichiometry: Often 1.0–1.5 equiv of strained alkyne to drive to completion.
• Temperature/time: 20–37°C, minutes to hours depending on ring strain and substituents.

Azide reduction to amine (general)

• Staudinger: PPh3 or water-soluble phosphines in THF/H2O or MeOH/H2O at RT; subsequent hydrolysis yields the amine.
• Catalytic hydrogenation: H2 (1–3 atm) over Pd/C in MeOH/EtOH at RT; ensure compatibility with the “LCL” core.

Note

• Verify the exact structure and any photolabile features of the “LCL” moiety on the CoA/Spec Sheet before selecting temperatures, light exposure, and catalysts.

Safety & Handling

Item-specific hazard statements and classifications

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

General safety guidance for PEG–azide linkers (literature/best practice)

• PPE: Wear lab coat, safety glasses, and appropriate gloves (nitrile). Use in a fume hood to avoid inhalation of vapors/aerosols and to contain spills.
• Organic azides: Many low-molecular-weight azides can be shock/heat sensitive; PEGylated azides are typically less energetic, but avoid excessive heat, friction, and impact. Do not distill to dryness. Keep away from strong reducing agents and heavy-metal salts that could form metal azides.
• Incompatibilities: Strong acids/bases may induce decomposition or PEG cleavage; strong oxidizers or reducing agents may react undesirably. Copper salts are used intentionally for CuAAC; avoid unintended metal contamination that could catalyze degradation.
• First aid overview: In case of skin/eye contact, rinse with water for at least 15 minutes; remove contaminated clothing. If inhaled, move to fresh air. If ingested, rinse mouth. Seek medical attention in all exposure cases. Defer to SDS for authoritative instructions.
• Spill response: Absorb with inert material, avoid ignition sources, and collect for disposal. Clean residues with suitable solvent while observing compatibility.

Storage and transport (from Product Data)

• Store at −20°C. Shipped in ice chest with ice pads. Allow to warm to room temperature in a desiccator before opening to minimize moisture uptake.

Solvent Selection

Applicability

• This section addresses dissolution and reaction media for PEG3–azide type linkers in general. Item-specific solubility is not provided.

General solvent guidance (literature)

• Polar aprotic solvents: DMSO and DMF provide excellent solubility for PEG-containing azides and are common for stock solutions and conjugations.
• Mixed aqueous systems: t-BuOH/H2O (1:1), MeOH/H2O, or acetonitrile/H2O are frequently used for CuAAC, balancing substrate solubility and catalyst activity.
• Pure aqueous media: Possible if the non-PEG portion is not overly hydrophobic; adding small percentages of co-solvent (DMSO, ethanol) often improves handling.
• Nonpolar solvents: Solubility is usually limited in alkanes; ethyl acetate and acetone can be moderate alternatives for workup and extractions.

Polarity and miscibility (general attributes)

• PEG3 confers moderate polarity and hydrogen-bond acceptor capacity; expect miscibility with polar organics and partial compatibility with water.

Comparison notes

• DMSO vs DMF: DMSO is higher boiling, very solvating, and greener from an exposure standpoint; DMF offers lower viscosity and easy removal but has stricter regulatory scrutiny.
• t-BuOH/H2O vs MeOH/H2O: t-BuOH systems often enhance CuAAC rates and reduce side reactions; MeOH/H2O improves solubility for some hydrophobic partners but may compete in metal coordination.

Tip

• Filter stock solutions (0.2 µm PTFE) and record concentration gravimetrically for accurate stoichiometry in conjugations.

Storage & Reconstitution

Storage (from Product Data)

• Store at −20°C.
• Shipped in an ice chest with ice pads to maintain low temperature during transit.

General handling and reconstitution (best practice; not item-specific)

• Moisture control: Allow vial to warm to room temperature in a desiccator before opening to prevent condensation and moisture uptake—PEG segments can be hygroscopic.
• Light exposure: If the “LCL” component is photolabile in your formulation, protect from light (amber vial, foil wrap). Confirm on the CoA/Spec Sheet.
• Stock solutions: Prepare concentrated stocks in anhydrous DMSO or DMF (e.g., 10–100 mM) under dry, inert atmosphere if feasible. Filter (0.2 µm PTFE) to remove particulates.
• Aliquoting: Dispense single-use aliquots and store at −20°C to minimize freeze–thaw cycles. Avoid repeated warming; record concentration gravimetrically for accuracy.
• Stability checks: Periodically assess by LC–MS or HPLC. Monitor for loss of azide band by IR (~2100 cm−1, literature) or appearance of hydrolysis products.

Disposal

• Dispose of azide-containing waste according to institutional protocols. Avoid introducing heavy-metal salts into azide waste streams to prevent formation of metal azides.

Documentation

• For definitive shelf-life, retest intervals, and any stabilizers, consult the lot-specific CoA/Spec Sheet and SDS.

Structure & Identity

Item-specific identifiers (from Product Data)

• CAS: 3033849-90-7
• 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.

Structural features and description (general/literature context, not item-specific)

• The name “LCL-PEG3-N3” typically denotes a construct containing:
  • A linker core ("LCL" occasionally denotes a linker scaffold; consult CoA/Spec Sheet for the exact identity).
  • A short polyethylene glycol spacer of three ethylene glycol units (PEG3).
  • A terminal azide functional group (–N3) for bioorthogonal ligation (e.g., click chemistry).
• Expected functional motifs (literature): ether repeats from PEG, and an organic azide terminus. If an LCL segment is photolabile in some catalog systems, light sensitivity can be relevant; confirm in the item CoA/Spec Sheet.
• 2D description (literature-style): a chain of three –CH2–CH2–O– units appended to a linker core on one end and capped with an –N3 substituent on the other.

Notes

• Because structure descriptors are not provided in the Product Data, treat the above as general guidance only and verify precise structure and stereochemistry on the CoA/Spec Sheet before experimental planning.

Synthetic Utility

Functional group and reactivity (general for PEG–azide)

• Azide terminus: Engages in CuAAC/SPAAC to form 1,2,3-triazoles; can be reduced to a primary amine (Staudinger or hydrogenation), enabling amide couplings and urea/carbamate formation.
• PEG3 spacer: Provides steric spacing and hydrophilicity, mitigating steric hindrance in surface and protein conjugations, and improving solubility of hydrophobic cores.

Typical transformations

• CuAAC with terminal alkynes (CuSO4/ascorbate/ligand) to build modular libraries rapidly.
• SPAAC with strain-activated alkynes for metal-free ligations on sensitive substrates.
• Staudinger ligation (with phosphines) for amide bond formation under aqueous conditions.
• Nucleophilic substitution: In some designs, internal azides arise from substitution on halides/mesylates; downstream, azide can be leveraged as a latent amine.

Retrosynthetic value

• Serves as a convergent handle: Keep the “LCL” portion constant while varying the alkyne partner to generate analog panels without re-derivatizing the core linker.

Operational guidance

• Ensure complete consumption of azide in click steps to avoid residual azide in the product (track by IR at ~2100 cm−1, literature). Excess alkyne or azide partner can drive conversions.
• If reducing to amine, quench phosphine oxide byproducts thoroughly (for Staudinger) and consider scavengers. For hydrogenation, select catalysts mindful of other reducible groups in the “LCL” core.

Target Specificity

This product is a small-molecule linker reagent, not an antibody, enzyme, or biological targeting agent. No target, epitope, clone, isotype, or species reactivity information is applicable.

• Item-specific targeting data: Not applicable.
• If used in bioconjugation, any “specificity” arises from the partner biomolecule or ligand you attach via click chemistry, not from the linker itself.

Frequently Asked Questions

How should this product be stored?

Store at ?20 °C. Freezer storage is required to maintain the specified shelf life.

How is this product shipped?

This product ships in an insulated container with ice pads. Unpack on arrival and transfer it to the storage condition stated above.

What are the CAS number, molecular formula and molecular weight?

The CAS Number is 3033849-90-7, the molecular formula is C32H45N7O6S, and the molecular weight is 655.81 g/mol.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.