Ethidium

A summary of the most common chemical descriptors (InChI Key and SMILES codes) for Ethidium are summarized together with 3D and 2D structures and relevant physico-chemical properties.

What is the Ethidium?

The molecule Ethidium presents a molecular formula of C21H20N3+ and its IUPAC name is 5-ethyl-6-phenylphenanthridin-5-ium-3,8-diamine.

Ethidium is a compound that is commonly used in molecular biology research as a fluorescent stain for DNA. It is a powerful intercalating agent, which means that it can insert itself between the base pairs of DNA and cause the molecule to fluoresce when exposed to ultraviolet (UV) light. This property makes it useful for visualizing DNA and RNA under a microscope or gel electrophoresis..

Ethidium has a high affinity for DNA and readily binds to the molecule, making it an effective stain for DNA. It is typically used in a concentration of 0.1-1.0 μg/mL and is applied to a sample of DNA or RNA in a solution. When the sample is exposed to UV light, the ethidium-stained DNA or RNA will fluoresce, allowing it to be visualized under a microscope or on a gel..

Ethidium has a number of limitations as a fluorescent stain. It is toxic to cells and can interfere with the normal function of DNA, so it must be used with caution. It is also relatively weak compared to other fluorescent dyes, so it may not provide as much signal intensity as other stains. Despite these limitations, ethidium is widely used in molecular biology research due to its high affinity for DNA and its ability to fluoresce when bound to the molecule..

Summary

From all the above, ethidium is a useful compound for visualizing DNA and RNA in research settings. Its ability to intercalate between the base pairs of DNA and cause the molecule to fluoresce makes it a valuable tool for studying the structure and function of these biomolecules..

3D structure

Cartesian coordinates

Geometry of Ethidium in x, y and z coordinates (Å units) to copy/paste elsewhere. Generated with Open Babel software.

2D drawing

 

Ethidium QTANTQQOYSUMLC-UHFFFAOYSA-O chemical compound 2D structure molecule svg
Ethidium

 

Molecule descriptors

 
IUPAC name5-ethyl-6-phenylphenanthridin-5-ium-3,8-diamine
InChI codeInChI=1S/C21H19N3/c1-2-24-20-13-16(23)9-11-18(20)17-10-8-15(22)12-19(17)21(24)14-6-4-3-5-7-14/h3-13,23H,2,22H2,1H3/p+1
InChI KeyQTANTQQOYSUMLC-UHFFFAOYSA-O
SMILESCC[n+]1c(-c2ccccc2)c2cc(N)ccc2c2ccc(N)cc21

Other names (synonyms)

IUPAC nomenclature provides a standardized method for naming chemical compounds. Although this system is widely used in chemistry, many chemical compounds have also other names commonly used in different contexts. These synonyms can come from a variety of sources and are used for a variety of purposes.

One common source of synonyms for chemical compounds is the common or trivial names, assigned on the basis of appearance, properties, or origin of the molecule.

Another source of synonyms are historical or obsolete names employed in the past, however replaced nowadays by more modern or standardized names.

In addition to common and historical names, chemical compounds may also have synonyms that are specific to a particular field or industry.

  • 2,7-DIAMINO-10-ETHYL-9-PHENYLPHENANTHRIDINIUM
  • 2,7-diamino-9-phenyl-10-ethylphenanthridinium
  • 3,8-Diamino-5-ethyl-6-phenylphenanthridinium
  • 3,8-diamino-5-ethyl-6-phenylphenanthridin-5-ium
  • 3546-21-2
  • 5-ethyl-6-phenyl-phenanthridin-5-ium-3,8-diamine
  • 5-ethyl-6-phenylphenanthridin-5-ium-3,8-diamine
  • AB00053825_07
  • BDBM200295
  • BDBM50105463
  • BRN 3627183
  • Babidium
  • CCG-35561
  • DivK1c_000940
  • EN464416SI
  • Ethidium
  • Ethidium cation
  • GTPL4569
  • Homidium cation
  • Homidium ion
  • IDI1_000940
  • KBio1_000940
  • KBio2_001980
  • KBio2_004548
  • KBio2_007116
  • KBioGR_000775
  • KBioSS_001980
  • NCGC00091387-03
  • NCGC00091387-04
  • NCGC00091387-05
  • NCGC00091387-06
  • NCI60_002180
  • NCI60_041857
  • NCIMech_000529
  • NCIOpen2_009324
  • NINDS_000940
  • NSC522843
  • NSC84423
  • Novidium
  • Phenanthridinium, 3,8-diamino-5-ethyl-6-phenyl-
  • Piperine & Ethidium bromide
  • Q27077234
  • RD-1572
  • Reserpine & Ethidium bromide
  • SBI-0051843.P002
  • cid_3624
  • homidium

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC119632
  • UNII-EN464416SI
  • DTXSID9048487
  • CHEMBL284328
  • CHEMBL48166
  • CHEBI:42478
  • SPBio_001554
  • UPCMLD-DP076
  • UPCMLD-DP076:001
  • SCHEMBL27609
  • Spectrum_001500
  • Spectrum2_001587
  • Spectrum4_000198
  • Spectrum5_001263

Physico-Chemical properties

IUPAC name5-ethyl-6-phenylphenanthridin-5-ium-3,8-diamine
Molecular formulaC21H20N3+
Molecular weight314.404
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity104.10
LogP5.3
Topological polar surface area55.9

LogP and topological polar surface area (TPSA) values were estimated using Open Babel software.

The n-octanol/water partition coeficient (Kow) data is applied in toxicology and drug research. Kow values are used, to guess the environmental fate of persistent organic pollutants. High partition coefficients values, tend to accumulate in the fatty tissue of organisms. Molecules with a log(Kow) (or LogP) greater than 5 are considered to bioaccumulate.

TPSA values are the sum of the surface area over all polar atoms or molecules, mainly oxygen and nitrogen, also including hydrogen atoms.

In medicinal chemistry, TPSA is used to assess the ability of a drug to permeabilise cells.

For molecules to penetrate the blood-brain barrier (and act on receptors in the central nervous system), TPSA values below 90 Å2 are required. Thus, molecules with a polar surface area greater than 140 Å2 tend to be poorly permeable to cell membranes.