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Nucleic Acids Research, 1979, Vol. 7, No. 7 1887-1900
© 1979

Articles

Nucleotide sequence of the 3'-noncoding region of alfalfa mosaic virus RNA 4 and its homology with the genomic RNAs

Ellen C. Koper-Zwarthoff, Frans Th. Brederod, Pauline Walstra and John F. Bol

Department of Biochemistry, State University of Leiden P.O. Box 9505, 2300 RA Leiden, The Netherlands

Received August 8, 1979. A 226-nucleotide fragment was derived from alfalfa mosaic virus RNA 4 (A1MV RNA 4), the subgenomic messenger for viral coat protein, and its sequence was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. The fragment contains the 3'-terminal 45 nucleotides of the coat protein cistron and the complete 3'-noncoding region of 182 nucleotides. The total length of RNA 4 was calculated to be 881 nucleotides.

A1MV RNAs 1, 2 and 3 were elongated with a 3'-terminal poly (A) stretch and subjected to sequence analysis by using a specific primer, reverse transcriptase and chain terminators. This revealed and extensive homology between the 3'-terminal 140 to 150 nucleotides of all four ALMV RNAs. Despite a number of base substitutions, the secondary structure of the homologous region is highly conserved. The observed homology indicates that, as with RNA 4, the sites with a high affinity for the viral coat protein are located at the 3'-termini of the genomic RNAs.


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