Nucleic Acids Research, 1983, Vol. 11, No. 4 947-960
© 1983
MOLECULAR BIOLOGY |
Satellite RNA of cucumber mosaic virus forms a secondary structure with partial 3'-terminal homology to genomal RNAs
Adelaide University Centre for Gene Technology, Department of Biochemistry, University of Adelaide Adelaide, South Australia 5001, Australia
Received January 4, 1983. Accepted January 21, 1983.
Sat-RNA is one of several replicating satellite RNAs which have been isolated from RNA encapsidated in cucumber mosaic virus (CMV) and which are totally dependent on CMV for replication. The 336 residue sequence of Sat-RNA obtained using the dideoxynucleotide chain termination and partial enzymic digestion procedures shows only a few short stretches (up to 11 residues) of sequence homology with one of the three CMV genomal RNAs so far sequenced. Sat-RNA has 88X sequence homology with another, previously sequenced, satellite RNA of CMV, CARNA 5. Analysis of partial digests of 5'– or 3'–32P-Sat-RNA with nuclease S1 or RNase T1 under non-denaturing conditions showed that only about 10% of the residues 1n Sat-RNA were cleaved. Further data on base-paired segments of Sat-RNA were obtained using digestion with RNase T1 followed by electrophoretic fractionati on of the resulting fragments under both non-denaturing and denaturing conditions. On the basis of this data, a complete secondary structure model is proposed for Sat-RNA with 52% of its residues Involved in base pairs. A prominent hairpin at the 3'–terminus of Sat-RNA shows considerable sequence and structural homology with parts of the 3'–terminal tRNA-like structure of the CMV genomal RNAs.