Sequence of the 5' end of the Sendai virus genome and its variable representation in complementary form at the 3' ends of copy-back defective interfering RNA species: identification of the L gene terminus.

Direct sequencing showed that the 5' termini of several defective interfering RNA species, both fusion and copy-back types, were homologous to the 5' terminus of the Sendai virus genome. Size analyses of spontaneously formed terminal duplexes (stems) of three copy-back defective interfering RNA species revealed variable extents of terminal complementarity, ranging from about 155 to 210 nucleotides. Direct sequencing of the 3' terminus of one of these copy-back RNA species demonstrated its complementarity to the 5'-terminal sequence of the virus genome. This copy-back sequence contained, in complementary form, the 5' terminus of the L gene, comprising the same sequence, 3'-AUUCUUUUU-5', that was previously identified at the 5' ends of the five other major Sendai virus genes.