Characterization and Comparison ofEscherichia coliTransfer RNAs by Graph Theory based on Secondary Structure

The origin of the genetic code: theories and their relationships, a review

“…Only one study conducted on 300 tRNAs sequences specific for 8 amino acids (Fitch and Upper, 1987) is in favour of the ambiguity reduction theory (Woese, 1965;Fitch and Upper, 1987). Other and equivalent analyses are in favour of the coevolution theory (Di Giulio, 1992a, 1994aChaley et al, 1999;Bermudez et al, 1999).…”

“…There are a number of observations and suggestions pointing out that the biosynthetic pathways of amino acids played a fundamental role in structuring the organization of the genetic code table (Nirenberg et al, 1963;Pelc, 1965;Jukes, 1966;Dillon, 1973;Wong, 1975Wong, , 1976Wong, , 1980Wong, , 1981Brack and Orgel, 1975;McClendon, 1986McClendon, , 1987Jurka and Smith, 1987a,b;Wachtershauser, 1988;de Duve, 1991;Miseta, 1989;Taylor and Coates, 1989;Danchin, 1989;Szathmary and Zintzaras, 1992;Morowitz, 1992;Szathmary, 1993;Di Giulio, 1992a,b, 1993, 1994, 1997a-c, 1999, 2000a,b, 2001, 2003Di Giulio and Medugno, 1998, 2000Di Giulio et al, 1994;Edwards, 1996;Chaley et al, 1999;Bermudez et al, 1999;Ardell and Sella, 2002;Zhu et al, 2003;Archetti, 2004;Klipcan and Safro, 2004), thus corroborating the coevolution theory.…”

Testing a biosynthetic theory of the genetic code: Fact or artifact?

“…[43][44][45]. In fact, they present variable evidence that evolutionarily related tRNA species are associated with biosynthetically related amino acids in extant organisms: none provides the explicit picture of tRNA evolution needed to test coevolution's specific model (e.g., see ref.…”

Reflections About Mathematical Chemistry

“…Among non-trivial molecular descriptors, topological indices are the simplest to compute, yet they contain much graph-theoretical information that is useful for quantitative structure-activity relationships (QSARs) in biochemical studies and drug design, or for quantitative structure-property correlations (QSPRs) for modeling and predicting physical-chemical properties of molecules. The molecular connectivity index v (Randic´, 1975; this is one of the most cited papers in the Journal of the American Chemical Society) and the average distance-based topological index J (Balaban, 1982) are among the best, and they have been used together in interesting biomedical applications such as finding arguments for the co-evolution of the genetic code with the development of biochemical pathways for arriving at the present 20 amino acids (Bermudez et al, 1999). With the index J and 12 other molecular descriptors, Lahana and his coworkers designed a new polypeptide that was 100 times more active as an immunosuppressor than the lead compound, which gave rise to a virtual library of about 250,000 candidate structures; the 13 molecular descriptors reduced it to 26 peptides (Grassy et al, 1998).…”