Cover: In plasmid R1, the synthesis of RepA protein is regulated at the translational level by an antisense RNA (CopA in red). Binding initiates within a subset of nucleotides in the hexanucleotide loop of the major CopA stem–loop, and its target site CopT. Propagation of the initial loop–loop helix extends into the upper stem regions, facilitated by the presence of bulged nucleotides to promote a stable and inhibitory complex. This complex is characterized by two intermolecular helices (green/purple) and two intramolecular helices in a four-helix junction structure, connected by single-stranded loop regions. Removal of the bulged residues, which inactivate the antisense RNA, does not prevent the initial formation of a loop–loop helix, but abolishes the subsequent transition towards the four-way junction [for additional comments see the paper by Kolb et al. in this issue: Nucleic Acids Res. (2001) 29 3145-3153].
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