Polynucleotide folding in yeast tRNA^Phe: Elucidation of short-, medium-, and long-range interactions of sugar-phosphate-sugar backbone and base using a "blocked" nucleotide probe

Abstract

It has recently been proposed that the repeating backbone nucleotide may be regarded as consisting of two blocks of equal magnitude representable by two virtual bonds. Implicit consideration of the nucleotide (ψ ,ψ ) and internucleotide (ω ',ω ) geometry that generate variety in polynucleotide conformations, and of the constancy of the repeating structural moieties (P-C4' and C4'-P) independent of the above rotations, has enabled us to utilize this scheme in the study of ordered structures such as di-, oligonucleotides and, most significantly, tRNA. The polynucleotide folding dictated by short-, intermediate-, and long-range interactions in the monoclinic and orthorhombic forms is described and compared through circular plots depicting the virtual bond torsions and distance plots constructed independently for backbone as well as bases. The torsions and the bond angles associated with the virtual bonds afford a clear distinction between ordered helical segments from loops and bends of tRNA. Lower virtual bond torsions (-60° to 60°) concomitant with higher values of virtual bond angles characterize various bend regions, while torsions around 160°-210° typify ordered helical strands. The distance plot elucidates the type of interaction associated with various sub-structures (helix-helix, helix-loop, and loop-loop) that form the constituents of different structural domains. Several other features such as the manifestation of the P₁₀ loop and the approximate twofold symmetry in the tRNA molecule are conspicuous on the distance plot.