Conformation of the 3'-end of beet necrotic yellow vein benevirus RNA 3 analysed by chemical and enzymatic probing and mutagenesis

Secondary structure-sensitive chemical and enzymatic probes have been used to produce a model for the folding of the last 68 residues of the 3'-non-coding region of beet necrotic yellow vein benevirus RNA 3. The structure consists of two stem-loops separated by a single-stranded region. RNA 3-derived transcripts were produced containing mutations which either disrupted base pairing in the helices or maintained the helices but with alterations in the base pairing scheme. Other mutants contained substitutions in single-stranded regions (loops or bulged sequences). With a few exceptions all three types of mutation abolished RNA 3 replication in vivo, suggesting that both secondary structure and specific sequences are required for efficient recognition of the 3'-terminal region of RNA 3 by viral RNA-dependent RNA polymerase.