Ethidium

Base Information

• Chemical Name: Ethidium
• CAS No.: 3546-21-2
• Molecular Formula: C21H20 N3
• Molecular Weight: 314.41
• Hs Code.: 2933990090
• UNII: EN464416SI
• DSSTox Substance ID: DTXSID9048487
• Nikkaji Number: J5.164K
• Wikidata: Q27077234
• NCI Thesaurus Code: C83806
• ChEMBL ID: CHEMBL48166
• Mol file: 3546-21-2.mol

Synonyms:Bromide, Ethidium;Bromide, Homidium;Ethidium;Ethidium Bromide;Homidium Bromide;Novidium

Chemical Property of Ethidium

Chemical Property:

• Boiling Point: °Cat760mmHg
• Flash Point: °C
• PSA: 56.42000
• Density: g/cm³
• LogP: 3.93400
• XLogP3: 4.2
• Hydrogen Bond Donor Count: 2
• Hydrogen Bond Acceptor Count: 2
• Rotatable Bond Count: 2
• Exact Mass: 314.165722651
• Heavy Atom Count: 24
• Complexity: 419

Purity/Quality:

99% ^*data from raw suppliers

ETHIDIUM 95.00% ^*data from reagent suppliers

Safty Information:

• Pictogram(s):  
• Hazard Codes: 

MSDS Files:

Useful:

• Canonical SMILES: CC[N+]1=C2C=C(C=CC2=C3C=CC(=CC3=C1C4=CC=CC=C4)N)N
• General Description: Ethidium, also known as homidium or ethidium cation, is a phenanthridinium compound with intercalating and fluorescent properties, making it useful in nucleic acid research. Studies have explored its derivatives, such as ethidium-arginine conjugates, which demonstrate antiviral activity against HIV-1 by targeting TAR RNA, and ethidium nucleosides, which serve as potential building blocks for oligonucleotide synthesis due to their stability and fluorescence. These applications highlight ethidium's versatility in biochemical and therapeutic contexts.

Technology Process of Ethidium

There total 4 articles about Ethidium which guide to synthetic route it. The literature collected by LookChem mainly comes from the sharing of users and the free literature resources found by Internet computing technology. We keep the original model of the professional version of literature to make it easier and faster for users to retrieve and use. At the same time, we analyze and calculate the most feasible synthesis route with the highest yield for your reference as below:

synthetic route:

Reference yield:

dihydroethidium (104821-25-2,38483-26-0) → ethidium (3546-21-2,89160-73-6)

Guidance literature:

With superoxide dismutase; xanthine oxidase; xanthin; Reagent/catalyst; Kinetics; Enzymatic reaction;

DOI:10.1002/anie.201002228

Reference yield:

hydroethidine (1314080-94-8) → 2-hydroxy-ethidium cation (854670-32-9) + ethidium (3546-21-2,89160-73-6)

Guidance literature:

With singlet oxygen; In acetonitrile; at 20 ℃; Solvent; Kinetics;

DOI:10.1016/j.cplett.2009.05.032

Reference yield:

dihydroethidium (104821-25-2,38483-26-0) → 2-hydroxy-ethidium cation (854670-32-9) + ethidium (3546-21-2,89160-73-6)

Guidance literature:

With glucose dehydrogenase; 2-hydroxynaphtho-1,4-quinone; D-glucose; 5-hydroxynaphtho-1,4-quinone; His₁₀-tagged NfsB; oxygen; NADPH; In aq. buffer; at 20 ℃; for 24h; pH=7.8; Kinetics; Darkness;

DOI:10.1002/cbic.201800071

upstream raw materials:

hydroethidine

C₂₁H₂₀⁽²⁾HN₃

dihydroethidium

Downstream raw materials:

3-Amino-5-ethyl-6-phenyl-8-[2-((R)-2-phenyl-[1,3]dioxan-4-yl)-acetylamino]-phenanthridinium

Refernces

Synthesis and antiviral activity of ethidium-arginine conjugates directed against the TAR RNA of HIV-1

10.1021/jm980728e

The study "Synthesis and Antiviral Activity of Ethidium-Arginine Conjugates Directed Against the TAR RNA of HIV-1" investigates the design and biological evaluation of ethidium-arginine conjugates targeting the TAR RNA of HIV-1 to inhibit viral replication. The researchers synthesized six ethidium derivatives with arginine side chains, aiming to disrupt the interaction between the Tat protein and TAR RNA. These conjugates were evaluated for their anti-HIV-1 activity in infected CEM-SS, MT4, and PBMC cells. Compounds 17 and 20 exhibited significant antiviral activity at micromolar concentrations without toxicity. The most active compound, 20, showed strong binding to TAR RNA, as evidenced by melting temperature studies and RNase footprinting experiments. Molecular modeling suggested that the ethidium moiety of compound 20 intercalates near the A17 residue, while the arginine side chain occupies the pyrimidine bulge, providing insights into the mechanism of action and potential for further development of HIV-1 inhibitors.

Synthesis of an ethidium nucleoside and its acyclic analog

10.1016/S0040-4039(03)00025-X

The research focuses on the synthesis and properties of ethidium nucleosides and their acyclic analogs. The purpose of this study was to prepare ethidium nucleosides that could potentially be used as building blocks for oligonucleotide synthesis, leveraging ethidium's ability to intercalate between DNA base pairs and its fluorescence properties. The researchers synthesized protected ethidium nucleosides, including 8-(3',5'-di-O-benzoyl-2'-deoxy-D-ribofuranosyl)-3-acetamido-5-ethyl-6-phenylphenanthridinium (5), 8-(3',5'-di-O-acetyl-2'-deoxy-D-ribofuranosyl)-3-acetamido-5-ethyl-6-phenyl-phenanthridinium (6), and the acyclic analog 8-[(3R)-1,3-dihydroxy-4-yl]-acetamido-3-amino-5-ethyl-6-phenyl-phenanthridinium (3). They found that only the acyclic derivative 3 was stable enough for potential use in oligonucleotide synthesis and exhibited absorption and emission properties comparable to underivatized ethidium. Key chemicals used in the synthesis process included 1,3,5-tri-O-acetyl-2-deoxy-D-ribofuranose, 1-chloro-3,5-di-O-benzoyl-2-deoxy-D-ribofuranose, 3,5-di-O-benzoyl-2-deoxy-D-ribofuranose, and various reagents for the protection and deprotection of functional groups, as well as coupling agents like HATU/HOAt and DCC/DMAP.