THE HYPERCUBE STRUCTURE OF THE GENETIC-CODE EXPLAINS CONSERVATIVE ANDNONCONSERVATIVE AMINO-ACID SUBSTITUTIONS IN-VIVO AND IN-VITRO

A representation of the genetic code as a six-dimensional Boolean hype rcube is described. This structure is the result of the hierarchical o rder of the interaction energies of the bases in codon-anticodon recog nition. In this paper it is applied to study molecular evolution in vi vo and in vitro. In the first case we compared aligned positions in ho mologous protein sequences and found two different behaviors: (a) Ther e are sites in which the different amino acids may be explained by one or two 'attractor nodes' (coding for the dominating amino acid(s)) an d their one-bit neighbors in the codon hypercube; and (b) There are si tes in which the amino acids correspond to codons located in closed pa ths in the hypercube, In the second case we studied the 'Sexual PCR'(1 ) experiment described by Stemmer [Stemmer (1994)] and found that the success of this combination of usual PCR and recombination is in part due to the Gray code structure of the genetic code.