Cytosine

Ball-and-stick Stick Space-filling

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13 atoms, 13 bonds.

IUPAC name: 6-amino-1H-pyrimidin-2-one
Molar mass: 111.104(13) g/mol
Atoms: 13
SMILES: C1=C(NC(=O)N=C1)N
InChIKey: OPTASPLRGRRNAP-UHFFFAOYSA-N
PubChem CID: 597

Made of

Structural formula of cytosine. Each unlabelled corner is a carbon atom, and the two hydrogens on carbon are not drawn. It shows which atoms are joined to which, not the shape. The model above shows the shape.

Cytosine is a base that both of the cell’s nucleic acids share: DNA and RNA each use it as one of their four letters. When a DNA sequence is printed as a string of letters, every C in it stands for cytosine.

The base is built on one ring of four carbon atoms and two nitrogen atoms. An amino group (NH₂) and a doubly bonded oxygen hang off the ring, and five hydrogen atoms sit around the edge. MeSH, the US National Library of Medicine’s subject vocabulary, calls it a pyrimidine base, a fundamental unit of nucleic acids; pyrimidine is the family name of its two-nitrogen ring. Its name under IUPAC (the International Union of Pure and Applied Chemistry) rules is 6-amino-1H-pyrimidin-2-one.

In double-stranded DNA its partner is fixed: cytosine on one strand faces guanine on the other. Unlike thymine, which RNA does without, cytosine appears in both DNA and RNA, and in each it spells the same letter C.

Structure and bonding

The viewer shows 13 atoms and 13 bonds, and in PubChem’s computed model every atom lies in one plane, the two amino hydrogens included. Turned edge-on, the molecule thins to a line. With Labels on, one ring nitrogen carries a hydrogen, and it sits between the carbon bearing the NH₂ group and the carbon bearing the oxygen.

In PubChem’s computed conformer the ring angles run from about 116° to 126°. Ball-and-stick draws three double bonds: C=O outside the ring, one C=C and one C=N inside it. Stick makes the alternation of double and single bonds easy to follow. Space-filling merges the spheres into a flat plate, with the red oxygen and the amino hydrogens at its rim.

Those fixed double lines are one drawing of the bonding, not the whole of it. According to Chem1, the π bonds in any system of alternating single and double bonds are delocalised, smeared over the conjugated stretch rather than parked between two atoms. A π bond is the second bond of a double bond. The model also shows the free base. In DNA and RNA the ring is attached to a sugar that links to a phosphate, forming a nucleotide.

Where it turns up

In DNA cytosine is one of four bases, alongside adenine, guanine and thymine; in RNA its companions are adenine, guanine and uracil.

ChEBI, a database of small molecules of biological interest, records it as a metabolite in humans and mice, in Saccharomyces cerevisiae and in Escherichia coli. The LOTUS natural-products database reports it in Camellia sinensis and Glycine max.

Outside the cell, cytosine’s monohydrate forms a lustrous solid, according to Haz-Map, a US occupational health database. The US Environmental Protection Agency lists it as active on its Toxic Substances Control Act inventory under the name 2(1H)-pyrimidinone, 6-amino-. It is also registered in the EU under REACH, the European chemicals registration law.

Why it matters

Inside the double helix, Chem1 notes, the sugar-and-phosphate backbones run along the outside and the bases point inwards, facing each other. Each cytosine meets a guanine on the opposite strand, and the pair forms one rung of the DNA ladder. Hydrogen bonds, which are weaker than covalent bonds, hold the rung. A hydrogen bonded to nitrogen carries a partial positive charge. Because the hydrogen atom is so small, that charge is dense enough to attract a lone pair, two unbonded outer electrons, on a nearby nitrogen or oxygen.

In the geometry of the helix, Chem1 explains, efficient hydrogen bonding is possible only for A–T and C–G, so those two pairs make up the alphabet of genetic information. A C on one strand fixes a G on the other, which is why a sequence can be written as a single string of letters.

Properties

Properties of cytosine Molar mass summed from IUPAC/CIAAW 2024 standard atomic weights; formula, atom and bond counts and PubChem's molecular weight from PubChem CID 597.
Property	Value	Unit	Source
Molecular formula (Hill order)	C₄H₅N₃O
Molar mass	111.104(13) g/mol	g/mol	IUPAC/CIAAW 2024
Carbon atoms	4
Hydrogen atoms	5
Nitrogen atoms	3
Oxygen atoms	1
Bonds	13
Single bonds	10
Double bonds	3
PubChem molecular weight	111.1 g/mol	g/mol	PubChem

Safety

Pure cytosine, handled as a laboratory powder, is an irritant. Most reports to the European Chemicals Agency (ECHA) give it the signal word Warning, for skin and serious eye irritation (86.4%) and possible respiratory irritation (84.7%). Eight of 59 ECHA reports (13.6%) find it does not meet the Globally Harmonized System (GHS) hazard criteria. The PubChem Laboratory Chemical Safety Summary for cytosine is the authoritative sheet for handling it.

Questions

What does the cytosine molecule look like in 3D?

A six-membered ring of four carbon and two nitrogen atoms, flat in PubChem's computed model, carries an NH₂ group and a C=O group. The drawing fixes three double bonds: C=O, one ring C=C and one ring C=N. According to Chem1, the π bonds in such a run of alternating single and double bonds are delocalised. In DNA and RNA the ring is part of a nucleotide, bonded to a sugar that carries a phosphate group.

What does cytosine pair with in DNA?

Cytosine pairs with guanine on the opposite strand, and adenine pairs with thymine. Hydrogen bonds between each pair of partners keep the two strands joined. Inside the helix, according to Chem1, only the A–T and C–G combinations can hydrogen-bond efficiently, so no other partner fits cytosine. According to the National Human Genome Research Institute, C–G pairs also bind more tightly than A–T pairs.

Is cytosine in RNA as well as DNA?

Yes. The NCI Thesaurus, the US National Cancer Institute's reference vocabulary, describes cytosine as a pyrimidine base found in both DNA and RNA. DNA's four bases are adenine, cytosine, guanine and thymine; RNA keeps adenine, cytosine and guanine and has uracil as its fourth. In both, the base belongs to a nucleotide, joined to a sugar, ribose in RNA and deoxyribose in DNA, which is attached in turn to a phosphate group.

What is the chemical formula of cytosine?

Its molecular formula is C₄H₅N₃O and its molar mass 111.1 g/mol. Its IUPAC (International Union of Pure and Applied Chemistry) name is 6-amino-1H-pyrimidin-2-one: amino for the NH₂ group, pyrimidin for the ring with two nitrogens, and 2-one for the carbonyl oxygen. ChEBI, a database of small molecules of biological interest, files it as an aminopyrimidine, a pyrimidone and a pyrimidine nucleobase, the family of bases found in nucleic acids.

Made of the same elements

C₅H₅N₅O Guanine 16 atoms, 17 bonds.
C₄H₄N₂O₂ Uracil 12 atoms, 12 bonds.
C₅H₆N₂O₂ Thymine 15 atoms, 15 bonds.
C₂H₅NO₂ Glycine 10 atoms, 9 bonds.
CO(NH₂)₂ Urea 8 atoms, 7 bonds.
C₅H₄N₄O₃ Uric acid 16 atoms, 17 bonds.
C₃H₇NO₂ Alanine 13 atoms, 12 bonds.
C₅H₉NO₄ Glutamic acid 19 atoms, 18 bonds.

All 25 compounds made of carbon, hydrogen, nitrogen and oxygen

C₈H₉NO₂ Acetaminophen 20 atoms, 20 bonds.
C₈H₁₀N₄O₂ Caffeine 24 atoms, 25 bonds.
C₈H₁₁NO₂ Dopamine 22 atoms, 22 bonds.
C₆H₁₃NO₂ Isoleucine 22 atoms, 21 bonds.
C₆H₁₃NO₂ Leucine 22 atoms, 21 bonds.
C₉H₁₁NO₂ Phenylalanine 23 atoms, 23 bonds.
C₁₀H₁₂N₂O Serotonin 25 atoms, 26 bonds.
C₉H₁₁NO₃ Tyrosine 24 atoms, 24 bonds.
C₁₁H₁₂N₂O₂ Tryptophan 27 atoms, 28 bonds.
C₉H₁₃NO₃ Epinephrine 26 atoms, 26 bonds.
C₁₂H₁₇NO DEET 31 atoms, 31 bonds.
C₁₃H₁₆N₂O₂ Melatonin 33 atoms, 34 bonds.
C₁₄H₁₈N₂O₅ Aspartame 39 atoms, 39 bonds.
C₁₄H₂₂N₂O Lidocaine 39 atoms, 39 bonds.
C₁₃H₂₁NO₃ Albuterol 38 atoms, 38 bonds.
C₁₇H₂₁NO Diphenhydramine 40 atoms, 41 bonds.
C₂₀H₂₄N₂O₂ Quinine 48 atoms, 51 bonds.