Computer building and folding of fictitious transfer-RNA sequences

In order to evaluate the common occurrence with which polynucleotides may adopt the cloverleaf configuration, 1150 random sequences were computer built and folded into their most stable secondary structure. Various constraints modulated the generation of the sequences: i) the base-pairing pattern, ii) the nucleotide composition, iii) the presence of assigned bases (modified or not) at certain sites, and iv) the chain length. In many cases, artificial tRNAs appear to require a more complex organization than a cloverleaf pairing scheme to achieve, as do natural molecules, the corresponding secondary structure. Moreover, the preferred foldings of sequences from 50 to 90 nucleotide long without an imposed pairing pattern usually contain two rather than three hairpin-loops. Implications concerning the emergence and the evolution of the protein-synthesis apparatus are discussed.