IUPAC Code Chart: Bases, Mnemonics & Complements
The IUPAC nucleotide codes are single letters that stand for a set of possible bases, so an ambiguous position can be written as one character. The four bases keep their letters (A, C, G, T / U), and eleven extra codes (R, Y, S, W, K, M, B, D, H, V, N) cover every other combination. This is the full table with the bases each code matches, its mnemonic and its complement.
| Code | Matches | Mnemonic / meaning | Group | Complement |
|---|---|---|---|---|
| A | A | Adenine | Base | T |
| C | C | Cytosine | Base | G |
| G | G | Guanine | Base | C |
| T | T | Thymine | Base | A |
| U | U | Uracil (RNA) | Base | A |
| R | A, G | puRine | Two bases | Y |
| Y | C, T | pYrimidine | Two bases | R |
| S | G, C | Strong (3 H-bonds) | Two bases | S |
| W | A, T | Weak (2 H-bonds) | Two bases | W |
| K | G, T | Keto | Two bases | M |
| M | A, C | aMino | Two bases | K |
| B | C, G, T | not A (B follows A) | Three bases | V |
| D | A, G, T | not C (D follows C) | Three bases | H |
| H | A, C, T | not G (H follows G) | Three bases | D |
| V | A, C, G | not T/U (V follows U) | Three bases | B |
| N | A, C, G, T | aNy base | Any | N |
How to read the codes
The two-base codes pair up by chemistry: R/Y split purines from pyrimidines, S/W split strong (three hydrogen bonds) from weak (two) base pairs, and K/M split keto from amino. The three-base codes are named for the base they exclude — B, D, H, Vare the letters following A, C, G and U in the alphabet, each meaning “not” that base. N matches anything.
Frequently asked questions
What does N mean in a DNA sequence?
N is the IUPAC code for any base — A, C, G or T. It is used where the base is unknown or could be any of the four, for example in degenerate primers or low-confidence sequencing positions.
What does R mean in DNA?
R stands for a puRine — either A or G. Its complement is Y (a pyrimidine, C or T).
What is the complement of an IUPAC ambiguity code?
Complement each code to the code representing the complementary base set: R↔Y, K↔M, B↔V, D↔H, while S, W and N are their own complements. For example the complement of R (A/G) is Y (T/C).
Why are degenerate bases used?
They compactly represent a position that can be more than one base — essential for designing degenerate primers, describing motifs and recording ambiguity in consensus sequences without writing out every possibility.
Learn more
Sources
- 1Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences: Recommendations 1984 (NC-IUB), Tables 1 and 2Nomenclature Committee of the International Union of Biochemistry (NC-IUB); Dixon HBF (Chairman), Lathe R (convenor) · IUBMB/IUPAC Biochemical Nomenclature Committees (official hosted text, Queen Mary University of London) · 1984 (published 1985)The entire CODES table, all 16 rows. Fetched and checked row by row. Table 1 gives the letter, the base set and the mnemonic: R puRine (A,G); Y pYrimidine (T,C); M aMino (A,C); K Keto (G,T); S Strong interaction 3 H bonds (G,C); W Weak interaction 2 H bonds (A,T); H not-G, follows G alphabetically (A,C,T); B not-A, follows A (G,T,C); V not-T/U, follows U (G,C,A); D not-C, follows C (G,A,T); N aNy (G,A,T,C) — every mnemonic string on the page matches this wording. Table 2 backs the whole Complement column: B<->V, D<->H, K<->M, A<->T, C<->G, and S, W, N are each their own complement (the page's R<->Y follows from the same table). The 'Group' badges (Base / Two bases / Three bases / Any) are SeqBench's own editorial grouping, not NC-IUB's.
- 2Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations 1984Cornish-Bowden A (byline on the Nucleic Acids Research printing; the recommendation is the work of the Nomenclature Committee of the IUB) · Nucleic Acids Research 13(9):3021-3030 · 1985The citable journal-of-record version of the same recommendation, for readers who want a DOI rather than a committee webpage. Verified that the DOI resolves (via Oxford Academic) to the correct title, volume, issue, pages and year; the full text is subscriber-only, so the free copy above is the one that actually shows the tables. The identical text also appeared in Eur J Biochem 150:1-5 (1985), Biochem J 229:281-286 (1985), J Biol Chem 261:13-17 (1986), Mol Biol Evol 3:99-108 (1986) and PNAS 83:4-8 (1986) — the qmul page lists all six.
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