Characterization and comparison of Escherichia coli transfer RNAs by graphtheory based on secondary structure

We have developed a model to characterize the tRNA structures of Escherichi a coil using graph theory. First of all, tRNAs were represented as graphs, whose vertices correspond to nucleotides and the edges to phosphodiester an d hydrogen bond linkages. Vertices and edges were weighted using the result s of a preliminary quantum study of the nucleotides and the possible coupli ng between pair bases using the semiempirical method AM1. For each vertex, we defined a nucleotide valence that measures the capability of forming hyd rogen bonds. Edges were differentiated by using bond orders. We have proposed weighted structural descriptors-closely related to molecul ar Randic connectivity and Balaban distance indices-as a distinctive charac teristic of each structure. Molecules were characterized by a set of weight ed structural descriptors and classified by a clustering method and discrim inant function analysis. Two main groups of tRNAs that correspond to the bi osynthetic amino acid pathways, in agreement with Wong's coevolution theory of the genetic code, were obtained. (C) 1999 Academic Press.