CONFORMATION OF THE 3'-END OF BEET NECROTIC YELLOW VEIN BENEVIRUS RNA-3 ANALYZED 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. Th e structure consists of two stem-loops separated by a single-stranded region. RNA 3-derived transcripts were produced containing mutations w hich either disrupted base pairing in the helices or maintained the he lices but with alterations in the base pairing scheme, Other mutants c ontained substitutions in single-stranded regions (loops or bulged seq uences), With a few exceptions all three types of mutation abolished R NA 3 replication in vivo, suggesting that both secondary structure and specific sequences are required for efficient recognition of the 3'-t erminal region of RNA 3 by viral RNA-dependent RNA polymerase.