Secondary and tertiary structural foldings in tRNA. A diagonal plot analysis using the blocked nucleotide scheme

Abstract

A distance plot obtained using the blocked nucleotide concept, which regards the repeating nucleotide moieties to be made up of two blocks of nearly equal magnitude, has permitted us to visualize the polynucleotide backbone folding in yeast tRNAPhe. The plot clearly manifests medium- and long-range tertiary interactions involving various structural domains. Apart from the well known TΨ-D loop interactions, other long-range interactions associated with the variable loop as well as the D loop are explicitly seen. Most importantly, the plot reveals an approximate two-fold symmetry in the molecule between the domains related to the tertiary interactions in addition to the symmetry between long helical domains. The different patterns on the plot are interpreted in terms of helix-helix, loop-helix and loop-loop interactions.