NUCLEOTIDE-SEQUENCE AT THE 5' END OF FOOT AND MOUTH-DISEASE VIRUS-RNA

Foot and mouth disease virus RNA has been treated with RNase H in the presence of oligo(dG) specifically to digest the poly(c) tract which lies near the 5′ end of the molecule (10). The short (s) fragment containing the 5′ end of the RNA was separated from the remainder of the RNA (L frag-ment) by gel electrophoresis. RNA ligaae mediated labelling of the 3′ end of S fragment showed that the RNase H digestion gave rise to molecules that differed only in the number of cytidylic acid residues remaining at their 3′ ends and did not leave the unique 3′ end necessary for fast sequence analysis. As the 5′ end of S fragment prepared from virus RNA is blocked by VPg, S fragment was prepared from virus specific messenger RNA which does not contain this protein. This RNA was labelled at the 5′ end using poly-nucleotide kinase and the sequence of 70 nucleotides at the 5′ end deter-mined by partial enzyme digestion sequencing on polyacrylaaide gels. Some of this sequence was confirmed from an analysis of the oligonucleotides derived by RNaae T digestion of S fragment. The sequence obtained indicates that there is a stable hairpin loop at the 51 terminus of the RNA before an initiation codon 33 nucleotides from the 5' end. In addition, the RNase T1 analysis suggests that there are short repeated sequences in S fragment and that an eleven nucleotide inverted complementary repeat of a sequence near the 3′ end of the RNA is present at the junction of S fragment and the poly(c) tract. © 1979 Information Retrieval Limited.