The Nucleotide Sequences of the 5′‐Terminal T1 Oligonucleotides of Semliki‐Forest‐Virus 42‐S and 26‐S RNAs are Different

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Abstract
To study the mechanism of the synthesis of Semliki Forest virus (SFV) 26-S RNA, we have isolated the 5′-terminal ‘cap’-containing RNase-T1-resistant oligonucleotide (T1 cap) from the genomic 42-S RNA and from the subgenomic 26-S RNA and determined their nucleotide sequences. The T1 caps were purified from 32P-labelled RNAs on two successive two-dimensional fractionation systems: (a) electrophoresis on cellulose acetate paper followed by homochromatography and (b) two-dimensional polyacrylamide gel electrophoresis. The T1 caps derived from the two RNAs had different mobilities in both systems. Their nucleotide sequence was found to be: m7G(5′)ppp(5′)ApUpUpGp-for the 42-S RNA and m7G(5′)ppp(5′)ApUpUpGp-for the 26-S RNA, respectively. Thus, it appears that the 26-S RNA is not formed by initiation of the RNA polymerase at the 3′ end of the negative-strand template followed by ‘cleavage and splicing’ or as the result of a ‘polymerase jump’. Our results, instead, favour the model of internal initiation of the polymerase on the 42-S negative-strand RNA template.