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In retrospect, a potential role for error coding in shaping the nucleotide alphabet seems obvious, and yet, with two notable exceptions, it appears to have been largely ignored; Szathmary recognized in his paper the relationship between donor-acceptor (D/A) patterns and replication errors (1992), while Yockey implicitly implied a role for error coding in nucleotide transmission, assigning 5-b representations to nucleotides (1992). Unfortunately, these assignments had no physicochemical basis, being based on mapping the natural alphabet to a code employed in an error-coding text. The model outlined in this paper melds these approaches, embracing a role for error coding, but one based on hydrogen/lone-pair patterns. The attraction of the error-coding description is that it offers a strikingly simple explanation of nature's choice of alphabet from among the set of potential nucleotides; optimal alphabets correspond to those in which the purine/pyrimidine feature relates to the D/A pattern as a parity bit. When this error-coding approach is coupled with chemical constraints, the natural alphabet of A, C, G, and T emerges as the optimal solution for nucleotides.
Engineering in Medicine and Biology Magazine, IEEE (Volume:25 , Issue: 1 )
Date of Publication: Jan.-Feb. 2006