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Nucleic Acids Research, 1980, Vol. 8, No. 23 5635-5647
© 1980

MOLECULAR BIOLOGY

Nucleotide sequences at the 5'-termini of the alfalfa mosaic virus RNAs and the intercistronic junction in RNA 3

Ellen C. Koper-Zwarthoff, Frans Th. Brederode, Gerrit Veeneman*, Jacques H. van Boom* and John F. Bol

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

Received September 9, 1980. Nucleotide sequences at the 5'-termini of the alfalfa mosaic virus genomic RNAs and the intercistronic junction in RNA 3 were deduced and compared to identify possible common recognition signals for replicating enzymes in the corresponsing minus-stranded viral RNAs. Homology between the 5'-terminal sequences is less than 11 nucleotides and no complementarity with the homologous sequence occurring at the 3'-end of the viral RNAs was observed. Homology between the 5'-terminus and intercistronic region in RNA 3 is compatible with the synthesis of subgenomic RNA 4 by internal initiation of transcription on the RNA 3 minusstrands. The sequence around the intercistronic junction can be folded into a very stable secondary structure.


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