5'-Terminal nucleotide sequence of Semliki forest virus 18S defective interfering RNA is heterogeneous and different from the genomic 42S RNA.

An 18S defective interfering (DI) RNA population was isolated from the cytoplasm of baby hamster kidney (BHK-21) cells infected with Semliki Forest virus from the 10th undiluted passage. The RNA was approximately 2000 nucleotides long and contained a 5'-terminal cap with the structure 7mGpppAp and a poly(A) tract. The DI RNA contained large TI oligonucleotides derived from both the 42S RNA-specific region and the 3' one-third of the genome common to 42S and 26S RNA. Several of the large oligonucleotides were present in nonequimolar ratios, suggesting that the RNA population is heterogeneous. As this population is approximately uniform in size, this suggests that the DI RNAs may be generated by internal deletions involving different regions of the genome. The 5'-terminal cap-containing RNase T1 oligonucleotide was isolated by two-dimensional gel electrophoresis from uniformly 32P-labeled RNA and shown to be heterogeneous. Five T1 caps with the structure 7mGpppA-U(A-U)nC-A-U-G(n = 4-8) were identified. The two major T1 caps (n = 4 and 6) comprised about 75% of the total yield of T1 caps. The T1 caps were different from the genomic 42S RNA T1 cap (7mGpppA-U-G), suggesting that the extreme 5' end of the genome is not conserved in this defective interfering RNA.