Defective interfering particles of Sindbis virus: V. Sequence relationships between SV STD 42 S RNA and intracellular defective viral RNAs

Abstract

The annealing of Sindbis virus RNAs was studied and optimal conditions were determined (50% formamide, 6× SSC, 60°). Using these conditions, we examined the sequence relationships between various Sindbis virus 32P-labeled single-stranded probe RNAs (42, 26, and a defective 22 S species) and five different driver double-stranded RNAs (22 S, RF-3, and the defective 18, 15, and 12 S species). It was concluded that each defective viral RNA represents a unique nonrepetitive fraction of the SV STD genome and that all of the sequences present in the smallest defective RNA are present in the larger defective RNAs generated earlier in the passage series. Furthermore, as they decreased in size, the defective RNAs retained about 1000 nucleotides from the 26 S region of the genome, but progressively smaller amounts from the non-26 S region. These results, along with observations of other workers, are consistent with the idea that defective viral RNAs are derived from the viral genome by a progressive process of internal deletion.