Ambiscript uses visual cues to encode key biochemical properties
The traditional DNA notation, which was formalized by the International Union of Pure and Applied Chemistry (IUPAC) in 19701, does little to convey the intrinsic biochemical features of the nucleotides they represent. Ambiscript is an alternative DNA notation, which is easy to learn and master because its character shapes and orientations reflect fundamental biochemical features of the nucleic acids (see figure). Ambiscript characters can be mastered using two rules:
- Baselines distinguish strong and weak binding pairs. Guanine and cytosine form a strong hydrostatic interaction with one another via three hydrogen bonds. Consequently, these bases are represented by symbols that are solidly rooted to the typographic baseline by a horizontal line. Conversely, the symbols for adenine and thymine, which exhibit a weaker hydrostatic interaction, only touch the baseline at two points.
- Orientations differentiate between purines and pyrimidines. Symbols representing the heavier purines (guanine and adenine) hang below the baseline while those encoding the lighter pyrimidines (cytosine and thymine) rise above it.
An important consequence of the AmbiScript character design is that complementary nucleotides are represented by pairs of symbols, which resemble one another when rotated 180°. This means that complementary sequences can be derived by simply rotating the strings of Ambiscript-encoded nucleotides 180°.
1 1970. IUPAC-IUB Commission on Biochemical Nomenclature (CBN). Abbreviations and symbols for nucleic acids, polynucleotides and their constituents. Recommendations 1970.Biochem. J. 120(3):449-454. (PMID: 5499957)