Biotin-sar-oh - ≥98% , CAS No.154024-76-7

CAS: 154024-76-7 Cat. No.: B1024586 PubChem CID: 20610692

GRADE & PURITY ≥98%

Storage

Room temperature

Specifications

Specifications & Purity

≥98%

Storage

Room temperature

Purity

≥98%

Names and Identifiers

Canonical Smiles

CN(CC(=O)O)C(=O)CCCCC1C2C(CS1)NC(=O)N2

IUPAC Name

2-[5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoyl-methylamino]acetic acid

InChIKey

FCDUPOLHSWBTFL-AUTRQRHGSA-N

INCHI

1S/C13H21N3O4S/c1-16(6-11(18)19)10(17)5-3-2-4-9-12-8(7-21-9)14-13(20)15-12/h8-9,12H,2-7H2,1H3,(H,18,19)(H2,14,15,20)/t8-,9-,12-/m0/s1

Isomeric SMILES

CN(CC(=O)O)C(=O)CCCC[C@H]1[C@@H]2[C@H](CS1)NC(=O)N2

PubChem CID

20610692

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Class Biotin and derivatives

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Class: Biotin and derivatives
• Subclass: Not available
• Intermediate Tree Nodes: Not available
• Direct Parent: Biotin and derivatives
• Alternative Parents: N-acyl-alpha amino acids Thienoimidazolidines N-acyl amines Imidazolidinones Thiolanes Tertiary carboxylic acid amides Thiophenes Ureas Azacyclic compounds Monocarboxylic acids and derivatives Dialkylthioethers Carboxylic acids Organonitrogen compounds Organic oxides Hydrocarbon derivatives Carbonyl compounds
• Molecular Framework: Aliphatic heteropolycyclic compounds
• Substituents: Biotin_derivative - N-acyl-alpha-amino acid - N-acyl-alpha amino acid or derivatives - Alpha-amino acid or derivatives - Thienoimidazolidine - Imidazolidinone - N-acyl-amine - Imidazolidine - Thiophene - Thiolane - Tertiary carboxylic acid amide - Carboxamide group - Urea - Carboxylic acid derivative - Carboxylic acid - Azacycle - Monocarboxylic acid or derivatives - Dialkylthioether - Thioether - Hydrocarbon derivative - Organic nitrogen compound - Organic oxygen compound - Carbonyl group - Organic oxide - Organooxygen compound - Organonitrogen compound - Aliphatic heteropolycyclic compound
• Description: This compound belongs to the class of organic compounds known as biotin and derivatives. These are organic compounds containing a ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring.
• External Descriptors: Not available

Data sources

1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.

DOI: 10.1186/s13321-016-0174-y

Chemical and Physical Properties

• Molecular Weight: 315.390 g/mol
• XLogP3: -0.100
• Hydrogen Bond Donor Count: 3
• Hydrogen Bond Acceptor Count: 5
• Rotatable Bond Count: 7
• Exact Mass: 315.125 Da
• Monoisotopic Mass: 315.125 Da
• Topological Polar Surface Area: 124.000 Ų
• Heavy Atom Count: 21
• Formal Charge: 0
• Complexity: 432.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 3
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 1

Application Protocols

No item-validated application protocols are provided in the Product Data. The following is general, literature-based guidance for amine biotinylation using EDC/sulfo-NHS.

Example: Aqueous EDC/sulfo-NHS coupling to an amine-bearing protein

• Materials: Biotin-sar-oh, EDC·HCl, sulfo-NHS, MES buffer (50 mM, pH 5.7), reaction buffer (PBS or HEPES, pH 7.8–8.2), desalting column, Tris or ethanolamine for quench.
• Stock solutions: Dissolve Biotin-sar-oh at 50–100 mM in anhydrous DMF or DMSO. Prepare fresh EDC (100–200 mM) and sulfo-NHS (100–200 mM) in water.
• Step 1 (Activation): In MES buffer, mix Biotin-sar-oh (final 1–5 mM) with 1.5 eq EDC and 2 eq sulfo-NHS. Incubate 10–20 min at 22–25°C.
• Step 2 (Coupling): Add activated mixture dropwise to the protein in pH 7.8–8.2 buffer (keep organic ≤10% v/v). Aim for 5–20 molar eq of biotin reagent per protein amine site, depending on desired labeling density. Incubate 1–2 h at RT.
• Step 3 (Quench/Cleanup): Add Tris (50 mM) or ethanolamine to quench residual active ester. Purify by desalting or dialysis. Assess labeling by HABA/Avidin assay, MS, or biotin blot.

Note: Optimize equivalents and time to balance labeling efficiency with protein activity. For small molecules/peptides, analogous conditions apply with monitoring by LC–MS/HPLC.

Biological Roles

Context (general biochemistry):

• Biotin (vitamin B7/H) is a covalently bound cofactor for biotin-dependent carboxylases, participating in CO2 transfer. Its high-affinity interaction with avidin/streptavidin (Kd ~10^−14–10^−15 M, literature) underpins a wide range of capture and detection technologies.

Relevance to Biotin-sar-oh (general; not a therapeutic claim):

• Biotin-sar-oh provides a compact biotin tag enabling site- or degree-controlled biotinylation of amine-bearing biomolecules. The sarcosine spacer can reduce steric congestion compared to direct biotinylation while keeping the tag short to minimize perturbation of biomolecule function.
• Conjugates produced with this building block retain the characteristic avidin/streptavidin binding of biotin, enabling affinity capture, immobilization on streptavidin-coated surfaces, and signal amplification in assay formats.

Usage domains (research use only):

• Proteomics/enrichment workflows (pull-downs, proximity labeling readouts after biotinylation).
• Nucleic acid labeling for hybridization capture and SPR/biolayer interferometry immobilization.
• Construction of biotinylated ligands, inhibitors, or probes for target engagement assays (no medical/clinical claims).

Note: Binding performance depends on conjugation site/stoichiometry and on spacer length; empirical optimization is recommended.

Buffer Applications

This product is not a buffering agent and is not typically used to prepare classical buffer systems.

Practical relevance (general guidance):

• For EDC/NHS activation of the carboxyl group, use amine-free buffers such as MES (25–100 mM, pH 5.0–6.5) to generate the active ester efficiently.
• For subsequent amide coupling to primary amines on biomolecules, adjust to pH 7.2–8.5 using phosphate, HEPES, or carbonate buffers. Avoid Tris or other primary amine buffers during activation/coupling, as they compete with the intended amine nucleophile.
• Include 0.1–0.5 M NaCl if needed to maintain protein solubility; add 5–10% DMF/DMSO only as required for solubility.

Buffer preparation tips (general):

• Degas buffers to reduce oxidative degradation for sensitive targets.
• Filter (0.22 µm) to remove particulates prior to bioconjugation workflows.

Green Alternatives

Green chemistry considerations typically center on solvent and coupling-reagent selection rather than the biotinylated scaffold itself.

Greener choices (literature/general):

• Solvent alternatives:
  • Replace DMF with bio-based dipolar aprotics such as Cyrene or GBL/GVL when compatible with substrates and reagents.
  • Favor water-rich media (≥80% water) for EDC/sulfo-NHS couplings when solubility allows, minimizing DMSO/DMF.
• Coupling reagents and byproducts:
  • EDC/sulfo-NHS generates water-soluble urea byproducts that are easier to remove than DCC-derived dicyclohexylurea (DCU); avoid DCC in favor of EDC where feasible.
  • Enzymatic ligation (e.g., transglutaminase for specific substrates) can, in select cases, offer milder and greener alternatives, though scope is narrower.
• Workup and waste:
  • Use aqueous extractions and dialysis when possible instead of large volumes of chlorinated solvents.

Balanced comparison (general):

• DMF vs water/DMF (9:1):
  • DMF provides superior solubility but higher environmental/health burden; partial substitution with water decreases VOC exposure.
• EDC/NHS vs HATU:
  • EDC/NHS is broadly effective in water-rich media with simpler waste; HATU can be higher yielding for hindered amines but entails less benign byproducts.

Note: Always validate green substitutions on small scale to confirm coupling efficiency and product integrity.

Pharmaceutical Uses

No therapeutic or clinical applications are claimed or supported for this item; it is supplied strictly for research use only.

General context (non-clinical, formulation/analytical relevance):

• Biotinylated molecules are widely used as affinity handles in analytical quality control assays, ligand-binding studies, and process analytics where streptavidin/biotin interactions facilitate capture and quantification.
• Biotin-sar-oh, as a compact biotin tag precursor, can be used to prepare biotinylated excipient mimics, analytical surrogates, or affinity probes for in-process testing and method development.
• In diagnostics R&D, biotinylated capture/detection reagents are commonly evaluated for solid-phase assay formats (e.g., streptavidin-coated plates, beads, or membranes).

Regulatory note:

• Pharmacopeial status, residual solvent limits, and any GMP compliance are not specified for this item; consult the CoA/Spec Sheet and your quality unit for suitability in regulated workflows.

Physical Properties

Item-specific specifications:

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

General/literature guidance (typical for biotinylated amino-acid derivatives; not a specification):

• Physical form is commonly a white to off-white solid.
• Solubility profile is often improved in polar aprotic solvents (e.g., DMF, DMSO) and in water at mildly basic pH where the terminal carboxyl is deprotonated (e.g., pH 8–9); limited solubility is typical in nonpolar solvents.
• Acidic/basic behavior: contains a carboxylic acid (acidic) and an amide (essentially non-basic); overall zwitterionic states are unlikely due to tertiary amide on sarcosine.
• Hygroscopicity: biotin conjugates are generally not strongly hygroscopic, but dry handling is still recommended to preserve coupling efficiency.

Practical notes (general):

• Prepare concentrated stocks in anhydrous DMSO or DMF, then dilute into aqueous buffers immediately prior to use to avoid premature hydrolysis during activation/coupling.

Quality and Grades

Item-specific (from Product Data):

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

Guidance on grades and what to expect (general):

• For bioconjugation building blocks, typical quality indicators include high chemical purity (often ≥95% by HPLC), identity confirmation by NMR/HRMS, and low residual solvents. Exact acceptance criteria vary by SKU and should be verified on the supplied CoA.
• Low water content and minimal hydrolytic impurities are important to maintain coupling efficiency and reduce side products. When not specified, best practice is to dry the solid under vacuum prior to moisture-sensitive steps (e.g., carbodiimide activation).
• If an inhibitor or stabilizer were used, it would be listed on the CoA; no stabilizer is specified for this item.
• UV cutoff or trace metal levels are generally irrelevant for this class; if critical for your assay (e.g., UV tracking or metal-catalyzed steps), confirm via CoA or request additional QC data.

Recommendations:

• Review the batch CoA for: assay (HPLC), identity (MS/NMR), residual solvents, and water (KF). If your application is quantitative labeling, consider running an incoming HPLC to benchmark purity before scale-up.

Reaction and Applications

Scope: As a biotinylated carboxylic acid bearing a short sarcosine spacer, Biotin-sar-oh is a versatile building block for introducing biotin onto amine-bearing molecules.

Common reactions (literature/general guidance):

• Carbodiimide-mediated coupling: activation with EDC (often with NHS or sulfo-NHS) to form an active ester in situ, followed by amide formation with primary amines on peptides, proteins, polymers, or surfaces.
• Uranyl or carbodiimide-free coupling to amines using uronium/phosphonium reagents (e.g., HATU, HBTU, PyBOP) in DMF with DIPEA or similar base.
• Pre-activation: conversion to isolated NHS ester (off-line) for later use in aqueous labeling.

Applications:

• Preparation of biotinylated peptides/oligonucleotide conjugates for capture/enrichment on avidin/streptavidin matrices.
• Fabrication of biotin-functionalized polymers and nanoparticles for affinity purification and assay immobilization.
• Surface biotinylation of amine-terminated self-assembled monolayers or resins.

Practical tips:

• Maintain pH 5.0–6.0 during EDC/NHS activation (minimizes O-acylisourea rearrangement); adjust to pH 7.5–8.5 for the coupling step with amines.
• Use freshly prepared activation solutions; moisture and time promote hydrolysis of active esters.
• Include a small excess (1.2–2.0 eq) of Biotin-sar-oh relative to amine to drive completion; optimize equivalents for sensitive biomolecules.

Reaction Conditions

General literature guidance for coupling the carboxyl group of Biotin-sar-oh to primary amines (optimize per substrate):

EDC/NHS aqueous coupling:

• Solvent/buffer: 25–100 mM MES, pH 5.5–6.0 for activation; later adjust to pH 7.5–8.5 for coupling. Keep organic cosolvent (DMF/DMSO) ≤10% v/v.
• Reagents: 1.0 eq Biotin-sar-oh, 1.1–2.0 eq EDC, 1.1–3.0 eq NHS or sulfo-NHS.
• Temperature/time: 20–25°C; activation 10–30 min; coupling 0.5–4 h (proteins) or up to overnight for sterically hindered amines.
• Quench: add Tris or ethanolamine after coupling to cap remaining active esters.

Uronium-mediated coupling (organic-rich):

• Solvent: anhydrous DMF (or DMSO).
• Base: DIPEA (2–4 eq relative to acid), optional catalytic HOAt.
• Reagents: HATU or HBTU (1.1–1.5 eq) with 1.0 eq Biotin-sar-oh and 1.0–2.0 eq amine.
• Temperature/time: 0–25°C, 0.5–3 h; monitor by LC–MS/HPLC.

Notes:

• Maintain low moisture to limit hydrolysis of intermediates.
• Excess of the biotin reagent helps drive completion for dilute bioconjugations.
• For sensitive biomolecules, minimize exposure to organic solvent and adjust ionic strength to preserve stability.

Safety and Handling

Authoritative safety information is provided in the SDS. The following summarizes available item data and general good laboratory practice.

Item-specific (from Product Data):

• GHS Classification: Not specified for this item; refer to SDS.
• Signal Word: Not specified for this item; refer to SDS.
• Hazard Statements (H-Statements): Not specified for this item; refer to SDS.
• Pictograms: Not specified for this item; refer to SDS.
• Storage Conditions: Room temperature.

General safety guidance (not a substitute for SDS):

• PPE: laboratory coat, safety glasses, and appropriate chemical-resistant gloves (e.g., nitrile). Work in a well-ventilated area; avoid generating dust/aerosols.
• Handling: keep container tightly closed and protected from moisture; avoid contact with strong oxidizers and strong acids/bases that may degrade amide/ureido functionalities.
• First aid (overview): if inhaled, move to fresh air; if on skin/eyes, rinse with water for several minutes; if ingested, rinse mouth and seek medical attention. Consult SDS for detailed instructions.
• Spill/leak response: avoid dust, collect solids with minimal disturbance, place in suitable container for disposal per institutional and regulatory guidance.
• Thermal stability: biotin conjugates are generally stable at ambient temperatures; avoid prolonged heating to prevent decomposition.
• Waste: dispose of unused material and contaminated consumables as organic laboratory waste in accordance with local regulations.

Solvent Selection

Applicability: Biotin-sar-oh is a small, polar, amide-containing carboxylic acid used for bioconjugation; solvent choice affects both solubility and coupling efficiency.

General solvent behavior (literature/general):

• Polarity class: polar protic/aprotic compatible; dissolves well in DMF and DMSO; aqueous solubility improves at mildly basic pH (carboxylate form).
• Miscibility profile: DMF and DMSO are water-miscible, enabling convenient dilution into aqueous buffers for EDC/NHS coupling.
• Typical buffers for coupling: MES (pH ~5.0–6.5) for activation; phosphate or HEPES at pH ~7.2–8.0 for amine coupling. Avoid primary amines (e.g., Tris) during activation/coupling steps to prevent quenching.

Choosing among options (general comparison):

• DMF: strong solvent power for peptides/proteins with minimal volatility; easy to blend with aqueous buffers.
• DMSO: excellent solubility; higher viscosity; can affect some bioassays at >5–10% v/v.
• Water-only: feasible at pH 8–9 if intrinsic solubility permits; may reduce need for organic cosolvent but can slow reactions.

Practical tips:

• Prepare a concentrated stock in anhydrous DMF or DMSO (e.g., 50–200 mM), then add slowly to the aqueous reaction to keep final organic content ≤10% v/v.
• Filter sterilize solutions (0.22 µm) for sensitive biological workflows if compatible.

Storage and Reconstitution

Item-specific (from Product Data):

• Storage Conditions: Room temperature.
• Shipped In: Not specified for this item; refer to CoA/Spec Sheet.
• Appearance: Not specified for this item; refer to CoA/Spec Sheet.

General guidance (supplementary; not a specification):

• Keep container tightly closed in a dry place; consider storing under inert gas or with a desiccant to minimize moisture uptake and preserve coupling performance.
• Protect from prolonged light and heat exposure.

Reconstitution (general suggestions):

• Prepare stock solutions in anhydrous DMF or DMSO (e.g., 50–200 mM). Vortex and, if needed, sonicate briefly to ensure complete dissolution.
• For aqueous use, dilute the organic stock into buffer immediately before activation/coupling. Avoid extended storage in aqueous solution to limit hydrolysis.

Solution storage (general):

• For short term (<24–48 h), store solutions at 2–8°C.
• For longer term, aliquot and freeze at −20°C or below to minimize freeze–thaw; thaw at room temperature and use promptly.

Always defer to the CoA/SDS for batch-specific stability and handling recommendations. Research use only.

Structure and Identity

Brief overview: Biotin-sar-oh is commonly understood (by name) as a biotinylated sarcosine (N-methylglycine) derivative bearing a free carboxylic acid terminus; it serves as a compact biotin tag/building block for amide-coupling to primary amines.

Item-specific (from Product Data):

• CAS: 154024-76-7
• PubChem CID: 20610692
• InChIKey: 78907 (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 structural features (literature/interpretation from name; not item-specific specifications):

• Functional groups: biotin bicyclic ureido/imidazolidone fused to a thiophane ring; an amide linkage to sarcosine (tertiary amide, N–CH3); terminal carboxylic acid (–CO2H) available for activation/coupling.
• Ring systems: bicyclic biotin core (ureido + tetrahydrothiophene/thiolane). No aromatic rings.
• Stereochemistry: biotin typically contains two stereocenters in the bicyclic core (retained in most biotin conjugates). Specific absolute configuration for this SKU is not specified; refer to CoA/Spec Sheet.
• 2D description in words: biotin core – amide – CH2–N(CH3)–CH2–CO2H (short, mildly polar spacer terminating in a carboxylate).

Synthetic Utility

Functional group leverage (general):

• Terminal carboxylic acid: convertible to active esters (NHS/sulfo-NHS), acid chlorides (less common in bioconjugation), or engaged directly in carbodiimide-mediated coupling to primary amines.
• Tertiary amide (sarcosine): chemically robust, minimizing side reactions and conferring a fixed, short spacer that can modulate hydrophilicity and sterics.
• Biotin core: introduces a high-affinity binding epitope for avidin/streptavidin without additional synthesis steps post-coupling.

Retrosynthetic/forward-planning considerations:

• Select this reagent when a very short linker is desired to reduce tag mobility while preserving strong biotin binding.
• For sterically hindered amines, consider more reactive coupling systems (HATU/HOAt) or pre-formed NHS esters derived from Biotin-sar-oh.
• Orthogonality: combine with protecting-group strategies on multi-functional scaffolds (e.g., Fmoc/Boc on other amines) to ensure selective coupling at the intended site.

Use cases:

• Late-stage modification of small molecules or peptides at a single exposed amine.
• Installation of biotin on amine-terminated PEGs, dendrons, or surfaces to prepare capture probes and affinity supports.

Purification:

• Reaction mixtures are often amenable to RP-HPLC purification (water/acetonitrile with 0.1% TFA or formic acid), or to aqueous workup followed by SPE for small molecules.

Target Specificity

This product is a small-molecule biotinylation building block and does not possess antibody/biologic target specificity parameters.

Item-specific data required for this section (antigen, clone, isotype, species reactivity) are not applicable. If your application involves capture on streptavidin/avidin surfaces, specificity arises from the biotin–(strept)avidin interaction rather than from an intrinsic biological targeting moiety.