Nucleic acid notation

[1] This universally accepted notation uses the Roman characters G, C, A, and T, to represent the four nucleotides commonly found in deoxyribonucleic acids (DNA).

Degenerate base symbols in biochemistry are an IUPAC[2][3] representation for a position on a DNA sequence that can have multiple possible alternatives.

Under the commonly used IUPAC system, nucleobases are represented by the first letters of their chemical names: guanine, cytosine, adenine, and thymine.

For example, S is used to represent the possibility of finding cytosine or guanine at genetic loci, both of which form strong cross-strand binding interactions.

Conversely, the weaker interactions of thymine and adenine are represented by a W. However, convenient mnemonics are not as readily available for the other ambiguity characters displayed in Table 1.

The spatial distribution of the circles made it far easier to distinguish individual bases and compare genetic sequences than IUPAC-encoded data.

[7] Rather than relying on spatially distributed circles to highlight genetic features, they exploited four geometrically diverse symbols found in a standard computer font to distinguish the four bases.

Ambigrams (symbols that convey different meaning when viewed in a different orientation) have been designed to mirror structural symmetries found in the DNA double helix.

[9] By assigning ambigraphic characters to complementary bases (i.e. guanine: b, cytosine: q, adenine: n, and thymine: u), it is possible to complement DNA sequences by simply rotating the text 180 degrees.

[10] An ambigraphic nucleic acid notation also makes it easy to identify genetic palindromes, such as endonuclease restriction sites, as sections of text that can be rotated 180 degrees without changing the sequence.