NUCLEOTIDE CORRELATIONS THAT SUGGEST TERTIARY INTERACTIONS IN THE TV-REPLACEMENT LOOP-CONTAINING MITOCHONDRIAL TRANSFER-RNAS OF THE NEMATODES, CAENORHABDITIS-ELEGANS AND ASCARIS-SUUM

In the predicted secondary structures of 20 of the 22 tRNAs encoded in mitochondrial DNA (mtDNA) molecules of the nematodes, Caenorhabditis elegans and Ascaris suum, the T psi C arm and variable loop are replac ed with a loop of 6 to 12 nucleotides: the TV-replacement loop. From c onsiderations of patterns of nucleotide correlations in the central re gions of these tRNAs, it seems highly likely that tertiary interaction s occur within five sets of binary and ternary combinations of nucleot ides that correspond in location to nucleotides known to be involved i n tertiary interactions in yeast tRNA(Phe) and other standard tRNAs. T hese observations are consistent with the nematode TV-replacement loop -containing mt-tRNAs being folded into a similar L-shaped functional f orm to that demonstrated for standard tRNAs, and for the bovine DHU (d ihydrouridine) arm replacement-loop-containing mt-tRNA(Ser(AGY)). Howe ver, the apparent occurrence in nematode mt-tRNAs of tertiary bonds co mmon to standard tRNAs contrasts with the situation in bovine mt-tRNA( Ser(AGY)) where the functional form is dependent on an almost unique s et of tertiary interactions. Because three of the proposed conserved t ertiary interactions in the nematode mt-tRNAs involve nucleotides that occur in the variable loop in standard tRNAs, it seems more likely th at in nematode mt-tRNAs it is the T psi C arm rather than the variable loop that has undergone the greatest proportional decrease in nucleot ide number.