Figure 2.

Double-bend RNA constructs used in this work. (A) The secondary structures of the yeast tRNA^Phe-A₅ constructs, designated E[tRNA^Phe:A₅]. Dashed extensions represent an additional 66 bp of RNA helix (4). Numerals 1 and 30 correspond to the numbering of native tRNA. (▾) Centers of the NheI sites created by the phasing/A₅ bulge insertions. N_n:N′_n refer to n additional (phasing) base pairs. Plasmids giving rise to specific transcripts are indicated to the left. (B) Phosphate backbone ribbon representations of the tertiary arrangements of two of the two-bend constructs; the darker ribbon represents the tRNA backbone (4, 16); the bulge is represented by an additional segment of backbone docked to two adjacent helices using insight (Molecular Simulations, Waltham, MA) for illustrative purposes; no attempt was made to find an energetically correct conformation. The centers of the tRNA and bulge bends are represented by solid and open arrowheads, respectively.