69075-42-9

Basic information

• Product Name: 5-Ethynyl uridine
• Synonyms: 5-Ethynyl uridine
• CAS NO: 69075-42-9
• Molecular Formula: C₁₁H₁₂N₂O₆
• Molecular Weight: 268
• EINECS: 500-100-4
• Mol File: 69075-42-9.mol
• Article Data: 8

Chemical Properties

• Appearance: /
• Density: 1.67±0.1 g/cm3(Predicted)
• Storage Temp.: -20°C
• Solubility: DMSO (Slightly), Methanol (Very Slightly, Heated, Sonicated)
• PKA: 8.29±0.10(Predicted)
• CAS DataBase Reference: 5-Ethynyl uridine(CAS DataBase Reference)
• NIST Chemistry Reference: 5-Ethynyl uridine(69075-42-9)
• EPA Substance Registry System: 5-Ethynyl uridine(69075-42-9)

Safety Data

• Hazardous Substances Data: 69075-42-9(Hazardous Substances Data)

Usage

Description

5-Ethynyl uridine (5-EU) is an alkyne-containing metabolic labeling reagent used to detect global RNA transcription temporally and spatially in both in-vitro and in-vivo with the modified nucleotide. The alkyne handler can be used for subsequent ligation to azide-containing molecules through a highly efficient click chemistry reaction.

Uses

Different sources of media describe the Uses of 69075-42-9 differently. You can refer to the following data:
1. 5-Ethynyluridine is used to help detect RNA synthesis in cells by its biosynthetic incorporation into newly transcribed RNA.
2. This alkyne-bearing metabolic labeling reagent can be used to measure RNA synthesis in proliferating cells. Once fed to cells, this nucleoside is incorporated during active RNA synthesis and can then be detected using a copper-catalyzed click reaction with fluorescent dyes. The cells can then be analysed by fluorescence imaging, flow cytometry or high content imaging analysis.

Upstream product

• 4105-38-8 Tri-O-acetyluridine 
• 84500-33-4 2',3',5'-tri-O-acetyl-5-iodouridine 
• 140914-90-5 2′,3′,5′-tri-O-acetyl-5-(ethynyl(2-trimethylsilyl))-uridine 
• 209254-94-4 2′,3′,5′-tri-O-acetyl-5-ethynyluridine 
• 58-96-8 uridine 
• 3052-06-0 1-β-D-arabinofuranosyl-5-iodouracil 
• 1024-99-3 5-iodouridine 
• 59989-18-3 5-ethynyluracil 

Downstream Products

• 58-96-8 uridine 
• 146-78-1 2-fluoroadenosine 
• 59989-18-3 5-ethynyluracil 
• 18646-11-2 α-D-ribofuranosyl-1-phosphate 

Relevant articles and documents

Investigation of C-5 alkynyl (alkynyloxy or hydroxymethyl) and/or N-3 propynyl substituted pyrimidine nucleoside analogs as a new class of antimicrobial agents

The resurgence of mycobacterial infections and the emergence of drug-resistant strains urgently require a new class of agents that are distinct than current therapies. A group of 5-ethynyl (6–10), 5-(2-propynyloxy) (16, 18, 20, 22, 24), 5-(2-propynyloxy)-3-N-(2-propynyl) (17, 19, 21, 23, 25) and 5-hydroxymethyl-3-N-(2-propynyl) (30–33) derivatives of pyrimidine nucleosides were synthesized and evaluated against mycobacteria [Mycobacterium tuberculosis (Mtb), Mycobacterium bovis (BCG) and Mycobacterium avium], gram-positive bacteria (Staphylococcus aureus and Enterococcus faecalis) and gram-negative bacteria (Escherichia coli, Salmonella typhimurium and Pseudomonas aeruginosa) alone and in combination with existing drugs in in vitro assays. Although several compounds exhibited marked inhibitory activity at a higher concentration against Mtb, M. bovis, S. aureus and E. faecalis, they displayed unexpected synergistic and additive interactions at their lower concentrations with antitubercular drugs isoniazid and rifampicin, and antibacterial drug gentamicin. The active analogues were also found to inhibit intracellular Mtb in a human monocytic cell line infected with H37Ra. Oral administration of 5-hydroxymethyl-3-N-(2-propynyl)-3′-azido-2′,3′-dideoxyuridine (32) and 5-hydroxymethyl-3-N-(2-propynyl)-2′,3′-dideoxyuridine (33) at a dose of 100?mg/kg for two weeks showed promising in vivo effects in mice infected with Mtb (H37Ra). No in vitro cytotoxicity of the test compounds was observed up to the highest concentration tested (CC50?>?300?μg/mL).

General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations

The biocatalytic synthesis of natural and modified nucleosides with nucleoside phosphorylases offers the protecting-group-free direct glycosylation of free nucleobases in transglycosylation reactions. This contribution presents guiding principles for nucleoside phosphorylase-mediated transglycosylations alongside mathematical tools for straightforward yield optimization. We illustrate how product yields in these reactions can easily be estimated and optimized using the equilibrium constants of phosphorolysis of the nucleosides involved. Furthermore, the varying negative effects of phosphate on transglycosylation yields are demonstrated theoretically and experimentally with several examples. Practical considerations for these reactions from a synthetic perspective are presented, as well as freely available tools that serve to facilitate a reliable choice of reaction conditions to achieve maximum product yields in nucleoside transglycosylation reactions.

Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates

We synthesized a small library of eighteen 5-substituted pyrimidine or 7-substituted 7-deazapurine nucleoside triphosphates bearing methyl, ethynyl, phenyl, benzofuryl or dibenzofuryl groups through cross-coupling reactions of nucleosides followed by triphosphorylation or through direct cross-coupling reactions of halogenated nucleoside triphosphates. We systematically studied the influence of the modification on the efficiency of T7 RNA polymerase catalyzed synthesis of modified RNA and found that modified ATP, UTP and CTP analogues bearing smaller modifications were good substrates and building blocks for the RNA synthesis even in difficult sequences incorporating multiple modified nucleotides. Bulky dibenzofuryl derivatives of ATP and GTP were not substrates for the RNA polymerase. In the case of modified GTP analogues, a modified procedure using a special promoter and GMP as initiator needed to be used to obtain efficient RNA synthesis. The T7 RNA polymerase synthesis of modified RNA can be very efficiently used for synthesis of modified RNA but the method has constraints in the sequence of the first three nucleotides of the transcript, which must contain a non-modified G in the +1 position.