Figure 5.

Predicted Intermolecular Secondary Structure Formed by the Extended 5′ and 3′ Fragments of RQ135⁻¹(−) RNA

The structure is based on the secondary structure model of RQ135 RNA (Munishkin et al. 1991). The foreign extensions are folded according to the lowest free energy criterion (Zuker and Stiegler 1981). Boldface letters depict the 5′ fragment, white letters in black circles depict the foreign extensions. Arrows indicate location of the precisely identified crossover sites along the 3′ fragment; brackets with matching shading indicate homologous stretches including the imprecisely localized crossover sites. Numbered letters refer to the type of recombinant sequence (Figure 4). The big arrow pinpoints the primary site of proposed attack of the 3′ fragment by the 3′ terminal hydroxyl of the 5′ fragment (see Discussion).