Name: 8-Azido-3,6-dioxaoctanoyl-AEEA
Brand: BOC Sciences
Rating: 5 (1 reviews)

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Synonyms

N3-AEEA-AEEA; 8-(8-Azido-3,6-dioxaoctanoylamido)-3,6-dioxaoctanoic acid; 2-[2-[2-[[2-[2-(2-Azidoethoxy)ethoxy]acetyl]amino]ethoxy]ethoxy]acetic acid

IUPAC Name

2-[2-[2-[[2-[2-(2-azidoethoxy)ethoxy]acetyl]amino]ethoxy]ethoxy]acetic acid

Canonical SMILES

C(COCCOCC(=O)O)NC(=O)COCCOCCN=[N+]=[N-]

InChI

InChI=1S/C12H22N4O7/c13-16-15-2-4-21-5-7-22-9-11(17)14-1-3-20-6-8-23-10-12(18)19/h1-10H2,(H,14,17)(H,18,19)

InChIKey

JSDQHVBNBHLKOJ-UHFFFAOYSA-N

Melting Point

34-39°C

Appearance

Light yellow oil/Low melting solid

Storage

Store at 2-8 °C

8-Azido-3,6-dioxaoctanoyl-AEEA, a versatile reagent in the realm of bioconjugation and click chemistry, boasts a myriad of applications. Here are four key applications narrated with elevated levels of perplexity and burstiness:

Protein Labeling: Serving as a staple in protein labeling endeavors, 8-Azido-3,6-dioxaoctanoyl-AEEA is a go-to choice for attaching various probes like fluorescent dyes or affinity tags to proteins. The azide group facilitates selective conjugation via click chemistry, ensuring precise and enduring attachments. This, in turn, aids in the visualization and tracking of proteins, a pivotal aspect of cellular and molecular biology studies.

Nucleic Acid Modification: Delving into nucleic acid modification, this reagent plays a vital role in appending functional groups to DNA or RNA molecules. By integrating 8-Azido-3,6-dioxaoctanoyl-AEEA, researchers can introduce biotin, fluorophores, or other reactive moieties for detection and analysis purposes. These modifications hold paramount importance in studies involving gene expression, molecular diagnostics, and genomic research, unraveling the intricacies of genetic mechanisms.

Bioorthogonal Chemistry: Stepping into the realm of bioorthogonal chemistry, 8-Azido-3,6-dioxaoctanoyl-AEEA emerges as a key player in introducing azide groups into biomolecules without disrupting natural biological processes. This breakthrough enables subsequent click reactions to take place selectively within living cells or organisms, a critical facet in imaging, drug delivery, and therapeutic advancements.

Surface Functionalization: Explore the world of surface functionalization, where 8-Azido-3,6-dioxaoctanoyl-AEEA shines in enhancing surfaces of various materials like nanoparticles, biomedical implants, and microarray chips. By engineering azide-functionalized surfaces, scientists can seamlessly attach a diverse array of biomolecules through click chemistry, paving the way for the development of biosensors, diagnostic tools, and cutting-edge materials for biomedical applications.

1. 3'-Deoxyribonucleotides inhibit eukaryotic DNA primase

S Izuta, M Kohsaka-Ichikawa, T Yamaguchi, M Saneyoshi J Biochem. 1996 Jun;119(6):1038-44. doi: 10.1093/oxfordjournals.jbchem.a021345.

In order to elucidate the biological activities of cordycepin (3'-deoxyadenosine) and related 3'-deoxyribonucleosides on eukaryotic DNA replication, the inhibitory effects of triphosphate derivatives of 3'-deoxyadenosine(3'-dATP), 8-azido-3'-deoxyadenosine(8-N3-3'-dATP), 3'-deoxyguanosine(3'-dGTP), 3'deoxyuridine(3'dUTP), 5-fluoro-3'deoxyuridine(5-F-3'-dUTP), 3'-deoxycytidine(3'-dcTP), and 5-fluoro-3'-deoxycytidine(5-F-3'dCTP) on DNA primase and replicative DNA polymerases alpha, delta, and epsilon purified from cherry salmon (Oncorhynchus masou) testes or calf thymus were examined. All analogs, except 8-N3-3'-dATP, showed strong inhibitory effects on DNA primase, but none of them inhibited DNA polymerases alpha, delta, or epsilon. Kinetic analysis revealed that the inhibition modes of them were competitive with respect to the incorporation of natural substrate that had the corresponding base moiety and non-competitive with respect to other substrates. Based on the kinetic data, we compared the affinities of 3'-dNTPs between DNA primase and RNA polymerases I and II, since 3'-dNTPs also inhibit eukaryotic RNA polymerases. Although the Ki values for DNA primase were much larger than those for RNA polymerases, the Ki/K(m) values, which indicate the affinity of the analog to the enzyme, were very similar.

2. Synthesis of the conjugation ready, downstream disaccharide fragment of the O-PS of Vibrio cholerae O:139

Shujie Hou, Pavol Kováč Carbohydr Res. 2011 Sep 6;346(12):1394-7. doi: 10.1016/j.carres.2011.02.011. Epub 2011 Feb 25.

The linker-equipped disaccharide, 8-amino-3,6-dioxaoctyl 2,6-dideoxy-2-acetamido-3-O-β-D-galactopyranosyluronate-β-D-glucopyranoside (10), was synthesized in eight steps from acetobromogalactose and ethyl 4,6-O-benzylidene-2-deoxy-2-trichloroacetamido-1-thio-β-D-glucopyranoside. The hydroxyl group present at C-4(II) in the last intermediate, 8-azido-3,6-dioxaoctyl 4-O-benzyl-6-bromo-2,6-dideoxy-2-trichloroacetamido-3-O-(benzyl 2,3-di-O-benzyl-β-D-galactopyranosyluronate)-β-D-glucopyranoside (9), is positioned to allow further build-up of the molecule and, eventually, construction of the complete hexasaccharide. Global deprotection (9→10) was done in one step by catalytic hydrogenolysis over palladium-on-charcoal.

3. Molecular characterization and verification of azido-3,8-dideoxy-d- manno-oct-2-ulosonic acid incorporation into bacterial lipopolysaccharide

Inga Nilsson, Kerri Grove, Dustin Dovala, Tsuyoshi Uehara, Guillaume Lapointe, David A Six J Biol Chem. 2017 Dec 1;292(48):19840-19848. doi: 10.1074/jbc.M117.814962. Epub 2017 Oct 9.

3-Deoxy-d-manno-oct-2-ulosonic acid (Kdo) is an essential component of LPS in the outer leaflet of the Gram-negative bacterial outer membrane. Although labeling of Escherichia coli with the chemical reporter 8-azido-3,8-dideoxy-d-manno-oct-2-ulosonic acid (Kdo-N3) has been reported, its incorporation into LPS has not been directly shown. We have now verified Kdo-N3 incorporation into E. coli LPS at the molecular level. Using microscopy and PAGE analysis, we show that Kdo-N3 is localized to the outer membrane and specifically incorporates into rough and deep-rough LPS. In an E. coli strain lacking endogenous Kdo biosynthesis, supplementation with exogenous Kdo restored full-length core-LPS, which suggests that the Kdo biosynthetic pathways might not be essential in vivo in the presence of sufficient exogenous Kdo. In contrast, exogenous Kdo-N3 only restored a small fraction of core LPS with the majority incorporated into truncated LPS. The truncated LPS were identified as Kdo-N3-lipid IVA and (Kdo-N3)2-lipid IVA by MS analysis. The low level of Kdo-N3 incorporation could be partly explained by a 6-fold reduction in the specificity constant of the CMP-Kdo synthetase KdsB with Kdo-N3 compared with Kdo. These results indicate that the azido moiety in Kdo-N3 interferes with its utilization and may limit its utility as a tracer of LPS biosynthesis and transport in E. coli We propose that our findings will be helpful for researchers using Kdo and its chemical derivatives for investigating LPS biosynthesis, transport, and assembly in Gram-negative bacteria.