Biotin Alkyne

Name: Biotin Alkyne
Brand: BOC Sciences
Rating: 5 (1 reviews)

CAS No.: 773888-45-2

Cat No.: BP-501030

Purity: NMR 1H (95%), TLC, functional testing 4.5

Biotin alkyne is a bifunctional chemical linker combining a biotin recognition handle with a terminal alkyne for site-selective conjugation. Structurally, it features a biotin moiety connected through an alkyl spacer to an alkyne group, enabling efficient attachment to azide-bearing partners via copper-catalyzed azide–alkyne cycloaddition (CuAAC) or related click chemistries, while preserving biotin’s high-affinity binding to streptavidin or avidin. In PROTAC and targeted protein degradation workflows, such a linker is valuable for modular assembly and for introducing affinity tags that facilitate detection, enrichment, or immobilization of PROTACs and related intermediates. The biotin handle can also support pull-down experiments to study ternary complex formation and substrate engagement, while the alkyne allows controlled placement of the biotin functionality without broadly perturbing the rest of the degrader architecture. Overall, it provides a practical tool for constructing and characterizing targeted degradation systems with robust analytical readouts.

Structure of 773888-45-2

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Category

PROTAC Linker

Molecular Formula

C13H19N3O2S

Molecular Weight

281.37

Appearance

colorless solid

* For research and manufacturing use only. Not for human or clinical use.

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Popular Publications Citing BOC Sciences Products

Purity

NMR 1H (95%), TLC, functional testing

Solubility

good in DMSO and DMF, low in water

Appearance

colorless solid

Storage

-20°C, sealed storage, away from moisture; In solvent, -80°C, 6 months; -20°C, 1 month (sealed storage, away from moisture)

Shipping

Room temperature in continental US; may vary elsewhere.

IUPACName

5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]-N-prop-2-ynylpentanamide

Synonyms

Biotin Propargylamide

InChI Key

JJXUHRONZVELPY-NHCYSSNCSA-N

InChI

InChI=1S/C13H19N3O2S/c1-2-7-14-11(17)6-4-3-5-10-12-9(8-19-10)15-13(18)16-12/h1,9-10,12H,3-8H2,(H,14,17)(H2,15,16,18)/t9-,10-,12-/m0/s1

SMILES

C#CCNC(=O)CCCCC1C2C(CS1)NC(=O)N2

1. Synthesis of alkyne-tagged and biotin-tagged Sortin1 as novel photoaffinity probes

Yoshihiro Ozeki, Rina Komatsu, Naohiro Kobayashi, Tamayo Yamaguchi, Kaori Sakurai Bioorg Med Chem Lett . 2018 May 15;28(9):1562-1565. doi: 10.1016/j.bmcl.2018.03.060.

Sortin1 is an inhibitor of vesicular biogenesis and transport, which is shared among eukaryotes and plants with an unknown mode of action. Toward exploration of its target proteins, we developed alkyne as well as biotin conjugated photoaffinity probes derived from Sortin1. Due to the presence of phenylketone moiety, Sortin1 was anticipated to serve as a photoreactive group in a similar manner to a commonly used photoreactive group, benzophenone. The core structure based on 5-oxo-1,4-dihydroindenopyridine was constructed in one step using three-component Hantzsch dihydropyridine synthesis. We demonstrated that Sortin1 displayed photocrosslinking reactivity against a model binding protein, which would be useful for capturing and detecting binding proteins.

2. Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition

Jennifer J L Hodas, John T Ngo, David A Tirrell, Daniela C Dieterich, Alborz Mahdavi, John D Bagert, Erin M Schuman, Peter Landgraf, Janek Szychowski J Am Chem Soc . 2010 Dec 29;132(51):18351-60. doi: 10.1021/ja1083909.

The azide-alkyne cycloaddition provides a powerful tool for bio-orthogonal labeling of proteins, nucleic acids, glycans, and lipids. In some labeling experiments, e.g., in proteomic studies involving affinity purification and mass spectrometry, it is convenient to use cleavable probes that allow release of labeled biomolecules under mild conditions. Five cleavable biotin probes are described for use in labeling of proteins and other biomolecules via azide-alkyne cycloaddition. Subsequent to conjugation with metabolically labeled protein, these probes are subject to cleavage with either 50 mM Na(2)S(2)O(4), 2% HOCH(2)CH(2)SH, 10% HCO(2)H, 95% CF(3)CO(2)H, or irradiation at 365 nm. Most strikingly, a probe constructed around a dialkoxydiphenylsilane (DADPS) linker was found to be cleaved efficiently when treated with 10% HCO(2)H for 0.5 h. A model green fluorescent protein was used to demonstrate that the DADPS probe undergoes highly selective conjugation and leaves a small (143 Da) mass tag on the labeled protein after cleavage. These features make the DADPS probe especially attractive for use in biomolecular labeling and proteomic studies.

3. Identification of recombinant AtPYL2, an abscisic acid receptor, in E. coli using a substrate-derived bioactive small molecule, a biotin linker with alkyne and amino groups, and a protein cross-linker

Keisuke Ohashi, Hideyuki Matsuura, Taichi E Takasuka, Tomoaki Anabuki, Kosaku Takahashi, Yusuke Ito Bioorg Med Chem Lett . 2019 Nov 1;29(21):126634. doi: 10.1016/j.bmcl.2019.126634.

Target protein identification of bioactive small molecules is one of the most important research in forward chemical genetics. The affinity chromatography technique to use a resin bound with a small molecule is often used for identification of a target protein of a bioactive small molecule. Here we report a new method to isolate a protein targeted with a bioactive small molecule using a biotin linker with alkyne and amino groups, protein cross-linker containing disulfide bond, and a bioactive small molecule with an azido group (azido probe). After an azido probe is associated with a target protein, the complex of a target protein and azido probe is covalently bound through the biotin linker by azide-alkyne Huisgen cycloaddition and protein cross-linker containing disulfide bond. This ternary complex is immobilized on an affinity matrix with streptavidin, and then the target protein is selectively eluted with a buffer containing a reducing agent for cleavage of disulfide bonds. This method uses a probe having an azido group, which a small functional group, and has the possibility to be a solution strategy to overcome the hindrance of a functional group introduced into the probe that reduces association a target protein. The effectiveness of the method in this study was shown using linker 1, 3'-azidoabscisic acid 3, and protein cross-linker containing a disulfide bond (DTSSP 5).

Biotin Alkyne is a versatile PROTAC linker building block designed to enable modular conjugation strategies that support targeted protein degradation workflows. Its biotin functionality facilitates robust handle-based assembly and compatibility with affinity enrichment approaches, while the alkyne provides a chemically addressable reactive site for constructing defined ternary or modular degraders. The molecule’s design supports efficient coupling to protein-binding ligands and downstream PROTAC synthesis, and the details below describe its structure and practical reactivity considerations for experimental use.

Structure: The linker incorporates a biotin-derived scaffold bearing an alkyne functional group, providing a rigid, chemically stable handle for subsequent conjugation. It contains heteroatoms typical of biotin chemistry and features a carbon–carbon triple bond suitable for click-type transformations. Overall, it is designed for solubility-compatible handling in common organic synthesis.

Reactivity: The terminal alkyne is well suited for copper-catalyzed azide–alkyne cycloaddition, enabling reliable attachment to azide-functional partners under standard click conditions. For PROTAC construction, the linker is typically used to connect ligand fragments via the alkyne handle, forming a triazole linkage that is generally stable under physiological-mimicking conditions. Commonly used catalysts and solvents are selected to balance reaction rate with preservation of sensitive functional groups.

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* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C₁V₁ = C₂V₂