Photoclick sphingosine , CAS No.1823021-14-2

CAS: 1823021-14-2 Cat. No.: P1440804 PubChem CID: 136212880

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

Photoclick sphingosine (Pacsph) is a photosensitizing and clickable sphingosine analog. Photoclick sphingosine is metabolized in cells into endogenous lipid metabolic pathways and can be visualized by its clickable alkyne group. Photoclick sphingosine can be used to study intracellular sphingolipid metabolism and subcellular localization.

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

Canonical Smiles

C#CCCCC1(N=N1)CCCCCCCCC=CC(C(CO)N)O

IUPAC Name

(E,2S,3R)-2-amino-13-(3-pent-4-ynyldiazirin-3-yl)tridec-4-ene-1,3-diol

InChIKey

CNCJUDANJBAFRY-WOKGBUJHSA-N

INCHI

1S/C19H33N3O2/c1-2-3-11-14-19(21-22-19)15-12-9-7-5-4-6-8-10-13-18(24)17(20)16-23/h1,10,13,17-18,23-24H,3-9,11-12,14-16,20H2/b13-10+/t17-,18+/m0/s1

PubChem CID

136212880

Application Protocols

General workflow (literature; for research use only)

1. Stock preparation

• Dissolve in anhydrous DMSO (or ethanol) to 5–20 mM. Store small aliquots at -20°C in amber vials. Avoid repeated freeze–thaw.

2. Cell labeling

• Dilute stock into prewarmed culture medium to a working concentration (e.g., 0.5–10 µM; optimize by cell type). Final DMSO ≤0.1–0.5%.
• Incubate 15–120 min to allow membrane incorporation and metabolism as desired.

3. UV photo-crosslinking

• Replace medium with fresh, prewarmed PBS or phenol-red–free medium if necessary. Irradiate at 350–365 nm for 5–20 min with cooling (ice or 4°C stage) to minimize heat.

4. Lysis and click tagging

• Lyse cells in appropriate buffer (detergent as needed). Perform CuAAC or SPAAC with biotin-azide/alkyne or fluorophore tags under standard conditions (e.g., CuSO4/THPTA/ascorbate for CuAAC).

5. Enrichment and analysis

• Enrich on streptavidin resin (if biotin tag), wash, and analyze by SDS-PAGE/Western blot or LC–MS/MS proteomics.

Controls

• Include no-probe, no-UV, and competition with excess native sphingosine to assess specificity. Validate cell health under chosen solvent, concentration, and UV conditions.

Note

• Parameters above are general literature guidance and should be adapted to your system.

Biological Roles

General background (literature; not item-specific claims)

• Sphingosine biology: Sphingosine is a central sphingolipid long-chain base found in eukaryotic membranes. It is N-acylated to ceramides and further converted to complex sphingolipids (sphingomyelin, glycosphingolipids). Phosphorylation yields sphingosine-1-phosphate (S1P), a potent signaling lipid.
• Functional roles: Modulates membrane microdomains, protein–lipid interactions, and intracellular signaling pathways; impacts endocytosis, apoptosis, and stress responses (context-dependent, model-dependent).
• Probe rationale: Photoclick sphingosine analogs are designed to mimic native sphingosine while providing two orthogonal handles: (1) a photoreactive group for covalent capture of transient interactions within membranes or protein pockets; (2) a click handle for sensitive tagging, enrichment, and imaging.
• Applications: Mapping sphingolipid–protein interactomes, tracking metabolic flux through ceramide and complex sphingolipids, and identifying binding sites within membrane proteins.

Important

• All uses are for research only. Biological outcomes are highly system-dependent; validate membrane incorporation and metabolic compatibility in your model (e.g., via LC–MS lipidomics following probe treatment). No clinical or diagnostic claims are made for this product.

Buffer Applications

Not a traditional buffer reagent.

Practical notes (general/literature)

• Working solutions: For biochemical assays, prepare stocks in DMSO/ethanol and dilute into physiological buffers (PBS, HBSS, or serum-containing media) with rapid mixing; keep final organic cosolvent low (typically ≤0.1–0.5% v/v, as permitted by your protocol).
• Carrier-assisted delivery: Complexation with fatty-acid–free BSA or cyclodextrins can improve aqueous dispersion. Alternatively, incorporate into liposomes or mixed micelles for in vitro binding assays.
• Light protection: Use amber tubes/foils during buffer preparation to prevent premature photolysis.

For buffer recipes, pH ranges, and ionic strength considerations, refer to the needs of your biological assay rather than this reagent itself.

Green Alternatives

Green chemistry considerations (general/literature)

• Solvent choices: Prefer ethanol or aqueous-compatible delivery systems over halogenated solvents. Minimize DMF/DMSO volumes in biological contexts and ensure proper waste segregation.
• Click chemistry: SPAAC (strain-promoted azide–alkyne cycloaddition) avoids copper catalysts, reducing metal waste and potential cytotoxicity; tradeoff is higher cost and sometimes slower kinetics.
• Energy use: Use efficient, narrow-band 365 nm LEDs rather than broad-emission mercury lamps to lower energy consumption and heat load.
• Scale: Conduct small-scale reactions to minimize hazardous waste from photolysis and copper-catalyzed click reactions.

Illustrative comparison (general)

• CuAAC vs SPAAC
  • CuAAC: Fast, robust, inexpensive; requires Cu(I) source and reducing agents; generates metal-containing waste; may be less suitable for live cells.
  • SPAAC: Metal-free, compatible with live cells; uses strained cycloalkynes (e.g., DBCO/BCN); costlier and sometimes slower.

Note

• This item is a specialized research probe; no direct “green” substitute matches its combined photo-crosslinking and click functionalities. Greener practice focuses on solvent selection, energy-efficient light sources, and catalyst-free click options where compatible.

Pharmaceutical Uses

No direct pharmaceutical or clinical use is claimed or intended.

General formulation/context (research only)

• Tool compound: Employed as an analytical probe in drug discovery workflows to characterize lipid–protein interactions, target engagement, and membrane partitioning of candidate molecules via photoaffinity labeling.
• Excipient status: Not applicable. This is not an excipient and has no pharmacopeial monograph.
• Manufacturing relevance: Can be used to develop and benchmark analytical capture/enrichment methods (e.g., click-biotin pull-down) within research settings.

Note: For research use only. Not for use in humans or diagnostics. Any incorporation into pharmaceutical development pipelines should be confined to preclinical research assays.

Physical Properties

Item-specific (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.
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Other specifications (bp/mp, density, refractive index): Not specified for this item; refer to CoA/Spec Sheet.

General/literature expectations for sphingosine-based photoclick probes (for context only)

• Physical state: Typically solid or viscous oil at ambient temperature; strongly hydrophobic with a small polar headgroup.
• Solubility: Poorly soluble in water; readily soluble in polar aprotic organic solvents such as DMSO, DMF, and moderately in ethanol/methanol; can be dispersed in aqueous buffers by premixing with carrier lipids, cyclodextrins, or low percentages of DMSO or nonionic detergents.
• LogP: High (hydrophobic long-chain base; exact value depends on substituents).
• Absorption: Photoactivatable groups (e.g., diazirines or aryl azides) absorb UV (commonly ~350–365 nm for diazirines; literature) and should be protected from light.
• pKa: The primary amine of sphingosine-like headgroups typically exhibits pKa in the 8–10 range (literature, environment dependent), affecting membrane association and charge state.

Important

• Do not treat the above literature values as specifications. For exact, item-specific parameters and QC limits, refer to the CoA/Spec Sheet.

Quality and Grades

Item-specific (from Product Data)

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

General guidance for this class of research reagents

• Research use: Labeled “For research use only” — not for human or animal diagnostic or therapeutic applications.
• Typical quality considerations for photoclick lipids:
  • Structural identity: Verified by NMR and HRMS; the presence and integrity of the photoreactive and click moieties are critical.
  • Purity: Monitored by HPLC/UPLC; impurities can include unmodified sphingoid bases or partially functionalized species.
  • Residual solvents and water: Low levels are preferable for stable storage and reproducible cellular uptake; exact limits are item-specific.
  • Light sensitivity: QC may include light-protection handling; packaging in amber vials is common.

What the grade implies

• If specified as “≥98%” or “HPLC-purified” on the CoA, this typically indicates suitability for cell-labeling workflows and downstream proteomics/chemoproteomics, with low UV background from impurities. Absent explicit values here, please refer to the CoA/Spec Sheet for this SKU.

Reaction and Applications

Applicability: Central for this probe class.

General/literature applications

• Photo-crosslinking: Upon UV irradiation (commonly 350–365 nm for diazirines), the probe forms highly reactive carbenes/nitrenes that covalently capture proximal biomolecules in membranes or protein complexes.
• Bioorthogonal tagging: The “click” handle enables post-irradiation conjugation to reporter tags (biotin, fluorophores) via CuAAC or SPAAC, facilitating enrichment (streptavidin) and visualization.
• Metabolic/pathway probing: Sphingosine analogs can be N-acylated by ceramide synthases to yield labeled ceramides; downstream metabolism can route to complex sphingolipids, enabling pathway mapping.
• Interactome discovery: Photocrosslinking in intact cells or membranes followed by click-chemistry tagging and MS-based proteomics to identify sphingolipid-binding proteins.

Practical tips (literature)

• Delivery: Prewarm media; add from a concentrated stock with rapid mixing to avoid precipitation; allow incorporation (e.g., 15–120 min) before UV exposure.
• Irradiation: Keep samples cold (on ice) to reduce thermal damage; use calibrated 350–365 nm lamps; typical exposures 5–20 min depending on lamp intensity and geometry.
• Controls: Include no-UV, no-probe, and inactive analog controls to distinguish specific from nonspecific binding.
• Click step: Use copper-chelating ligands (e.g., THPTA/TBTA) for CuAAC to enhance kinetics and reduce protein oxidation; consider copper-free SPAAC for live-cell compatibility.

Note: Parameter ranges are literature guidance and should be optimized per system.

Reaction Conditions

General/literature guidance (not item-specific specifications)

• Photo-crosslinking:
  • Wavelength: 350–365 nm (diazirine-type) or 302–312 nm (aryl azide; verify for your analog).
  • Temperature: Often 0–4°C for live cells or lysates to limit thermal damage; ambient for robust in vitro systems.
  • Time: 5–20 minutes depending on light source intensity and sample geometry.
  • Atmosphere: Ambient; ensure adequate cooling and uniform illumination.
• Click chemistry (CuAAC):
  • Typical reagents: Azide/alkyne tag (50–100 µM), CuSO4 (0.5–1 mM), ligand such as THPTA/TBTA (1–2 mM), sodium ascorbate (1–5 mM) to generate Cu(I).
  • Solvent/buffer: Aqueous PBS/TBS with 1–10% DMSO or t-BuOH/H2O mixtures; pH ~7–8.
  • Time/temperature: 15–60 min at room temperature with gentle mixing.
• Click chemistry (SPAAC):
  • Reagents: Strained alkyne (e.g., DBCO, BCN) 5–50 µM; no copper required.
  • Conditions: Aqueous buffers at RT; reaction times 30–120 min depending on partners.

Controls and validation

• Include no-UV/no-probe controls; assess incorporation via LC–MS or fluorescence post-click. Optimize concentrations to balance labeling efficiency and minimal perturbation of membranes.

Safety and Handling

Item-specific (from Product Data)

• Signal word: Not specified for this item; refer to SDS.
• H-statements: Not specified for this item; refer to SDS.
• GHS classification/pictograms: Not specified for this item; refer to SDS.
• Storage: Store at -20°C. Protect from light. Shipped in ice chest with ice pads.

General safety guidance (literature/standard practice)

• Photoactivity: Photoreactive groups (e.g., diazirines, aryl azides) generate reactive intermediates under UV. Handle in low light or amber containers; avoid unnecessary UV/strong visible light exposure.
• PPE: Lab coat, safety glasses, and appropriate gloves (e.g., nitrile). Use in a fume hood to avoid inhalation of solvent vapors and potential reactive byproducts.
• Incompatibilities: Strong oxidizers; avoid UV exposure around incompatible materials. For click derivatization using CuAAC, manage copper salts carefully and prevent exposure to reducing agents without proper controls.
• 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 advice. Always follow institutional SOPs.
• Waste: Dispose of copper-containing click reaction waste and photolysis mixtures as hazardous organic waste per local regulations.

Authoritative information

• Always consult the product’s SDS for definitive hazard, first-aid, and disposal guidance.

Solvent Selection

Applicability: Highly relevant for hydrophobic lipid probes.

General/literature guidance

• Polarity and miscibility: Photoclick sphingosine analogs are amphiphilic, but dominated by a hydrophobic long chain; they dissolve well in DMSO and DMF, moderately in ethanol/methanol, and poorly in water. They can be delivered to aqueous systems by cosolvents or carriers.
• Recommended stock solvents: Anhydrous DMSO (common), DMF, or ethanol. Prepare concentrated stocks (e.g., 5–20 mM) and dilute into media/buffers with immediate mixing to avoid precipitation.
• Aqueous delivery strategies:
  • Cosolvent approach: Final DMSO ≤0.1–0.5% v/v for live cells (institutional limits vary).
  • Carrier systems: Complex with fatty-acid–free BSA, cyclodextrins (e.g., MβCD), or incorporate into liposomes/mixed micelles with mild nonionic detergents (e.g., 0.01–0.1% Triton X-100 or Pluronic; verify compatibility).
• Light sensitivity: Use amber vials and minimize light exposure during handling and solvent exchange.

Comparison (literature-based, general)

• DMSO: Highest solvating power; may affect cell membranes at >0.5%.
• Ethanol: Biocompatible at low %; lower solvency; faster evaporation.
• DMF: Strong solvency but less favored for live cells; useful for in vitro reactions (click chemistry).

Note: Select solvents based on your biological system and downstream click chemistry. Verify solubility and compatibility empirically.

Storage and Reconstitution

Item-specific (from Product Data)

• Storage conditions: Store at -20°C.
• Shipping: Shipped in an ice chest with ice pads.

General handling best practices for photoclick lipid probes

• Light protection: Store and handle in amber vials; minimize exposure to ambient light to preserve the photoreactive group.
• Stock solutions: Prepare concentrated stocks (e.g., 5–20 mM) in anhydrous DMSO, DMF, or ethanol. Aliquot into single-use portions to avoid repeated freeze–thaw cycles.
• Stability: Keep tightly closed under inert gas (optional) and dry; avoid moisture ingress. Do not store working dilutions for extended periods.
• Thawing: Thaw aliquots briefly at room temperature, mix gently, and return unused portions to -20°C promptly.
• Aqueous use: Immediately dilute stocks into buffers/media with vigorous mixing to prevent precipitation; verify final solvent tolerance for your system.

Reconstitution specifics

• Any item-specific reconstitution concentration, solvent, or stabilizer details: Not specified for this item; refer to CoA/Spec Sheet.

Documentation

• For definitive shelf life, retest intervals, and stability-indicating methods, consult the product CoA and SDS.

Structure and Identity

Item-specific (from Product Data)

• Product name: Photoclick sphingosine (SKU: P1440804)
• CAS: 1823021-14-2
• PubChem CID: 136212880
• InChIKey: 48553 (as provided)
• 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.

General chemistry/literature description

• Structural class: Sphingosine-based probe bearing a photoreactive group (commonly diazirine) and a bioorthogonal “click” handle (e.g., alkyne or azide) for post-labeling enrichment/visualization.
• Core features: Long-chain amino alcohol backbone analogous to D-erythro-sphingosine (trans-alkene, 1,3-amino-diol motif), functionalized with a photoactivatable moiety and a click tag.
• 2D structure (described): A C18-like hydrophobic chain containing one double bond; the polar headgroup features a primary amine and vicinal secondary alcohol; an additional small ring (diazirine) or aryl–azido substituent provides UV-activatable crosslinking, while a terminal alkyne or azide enables copper-catalyzed or strain-promoted cycloaddition.

Notes

• Exact regiochemistry, stereochemistry, and tag placement can vary among photoclick sphingosine analogs; consult the CoA/Spec Sheet for this item’s definitive structure.

Synthetic Utility

General chemistry perspective (literature; probe-centric)

• Functional handles: The headgroup primary amine and secondary alcohols of the sphingoid backbone allow derivatization (e.g., N-acylation to ceramides, phosphorylation to S1P analogs). The built-in click handle enables modular conjugation to dyes, affinity tags, and crosslinking handles.
• Transformations:
  • N-Acylation: Generate photoclick ceramide analogs using activated fatty acids (acid chlorides, NHS esters) under mild base; preserves photo/click functionality for downstream studies.
  • Bioorthogonal ligation: CuAAC or SPAAC to attach biotin/fluorophores post-irradiation for enrichment/imaging.
  • Solid-support capture: Click to azide/alkyne-functionalized beads for on-bead digestion and MS proteomics.
• Retrosynthetic value: Serves as a versatile node for constructing a family of sphingolipid probes with varied chain lengths, saturation patterns, and reporter tags while maintaining a conserved photo-crosslinking capability.

Caveats

• Protect photoactive groups during synthesis and workup (amber glass, low light). Select coupling conditions that avoid radical initiators or extended UV exposure to prevent premature decomposition.

Target Specificity

Not applicable.

• This product is a small-molecule lipid probe, not an antibody or affinity reagent with defined antigen specificity. It captures proximal interaction partners upon photoactivation in a proximity-dependent fashion rather than binding a single target epitope.
• Any protein “targets” identified will be experiment- and context-dependent; validate with orthogonal assays (competition with native sphingosine, inactive analogs, mutagenesis).

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 1823021-14-2. InChIKey CNCJUDANJBAFRY-WOKGBUJHSA-N.

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.