A degenerate oligonucleotide is a mixture of sequences that differ in one or more positions. If there is a single degenerate position that contains only purines, the mixture contains roughly equal amounts of two sequences (21). If there are ten completely random degenerate positions, the mixture contains over a million sequences (410). To describe these degenerate positions, one of eleven possible single-letter, mixed-base codes is used. The standard nomenclature for these degenerate positions is defined by the International Union of Pure and Applied Chemistry (IUPAC).
| Symbol | Bases | Origin of designation |
| R | A, G | puRine |
| Y | C, T | pYrimidine |
| M | A, C | aMino |
| K | G, T | Keto |
| S | C, G | Strong interaction (3 hydrogen bonds) |
| W | A, T | Weak interaction (2 hydrogen bonds) |
| H | A, C, T | not G, H follows G in the alphabet |
| B | C, G, T | not A, B follows A |
| V | A, C, G | not T (not-U), V follows U |
| D | A, G, T | not C, D follows C |
| N | A, C, G, T | aNy |
