Nucleotide sequence homology of thirteen tobamovirus RNAs as determined by hybridization analysis with complementary...

The extent of RNA sequence homology between 13 isolates of tobamoviruses has been estimated by hybridization analysis using radioactive complementary DNA. Hybrid formation between complementary [3H]DNA prepared against 7 of the tobamovirus RNAs and the RNAs of the 13 isolates was assayed with the single-strand-specific S1 nuclease. The presence of mismatched regions in the DNA: RNA hybrids was shown by variation of the stringency of the conditions for the hybridization and S1 nuclease assay. The data obtained have allowed the allocation of the 13 isolates into five groups on the basis of significant sequence homology between members of each group. Members of two of these groups were further divided into subgroups on the basis of differences in the hybridization data. Although hybridization analysis using labeled complementary DNA is considered the method of choice at present for estimating sequence homology between viral RNAs, the limitations inherent in any hybridization approach are discussed.