Mapping and sequencing of RNAs without recourse to molecular cloning: application to RNAs of the Sabin 1 strain of poliovirus and its defective interfering particles.

Complementary DNA to the genome of the Sabin 1 strain of poliovirus was prepared by reverse transcription with oligo(dT)10 as a primer and separated into six classes of DNA by their size. Each class of the DNA, after digestion with restriction endonuclease HaeIII, was analyzed by two-dimensional polyacrylamide gel electrophoresis. Comparison of the patterns of the restriction fragments led us to compose a possible arrangement of the restriction fragments on the viral genome. Sequence analysis of these fragments indicated that the arrangement was consistent with the known total nucleotide sequence of the genome. In the determined sequences, two bases were observed to differ from those of a cloned complementary DNA of the Sabin 1 genome. This suggested that the sequence of the cloned DNA reflected that of a mutated virus genome that was a minor component in the virus inoculation stock. The genomes of defective interfering particles generated from the Sabin 1 strain were also analyzed by this technique. The results suggested that the RNAs lacked an internal region of the Sabin 1 RNA encoding viral capsid proteins. The location of the deletion was further confirmed by determination of the nucleotide sequence of a cloned complementary DNA copy of the defective interfering particle RNA. Thus, the method described here is useful for mapping and sequencing of RNAs and for knowing whether cloned cDNAs represent the major population of RNA molecules or not.