Characterization of dna complementary to nucleotide sequences at the 5′-terminus of the avian sarcoma virus genome

The 5′-end of the genome of avian sarcoma virus (ASV) contains a sequence of nucleotides which is the initial template for transcription by RNA-directed DNA polymerase. We have prepared DNA complementary to this sequence (cDNA5,) and have characterized the sequence by chemical analysis and molecular hybridization. The length of cDNA5, (00 nucleotides) provides an estimate of the distance from the primer for DNA synthesis (tRNAtrp) to the 5′-terminus of the genome. As reported previously by other investigators, transcription of DNA from the genome of ASV in vitro can be arrested at preferred sites short of the 5′-terminus by reduction in the concentration of either dCTP or dGTP. The nucleotide sequence complementary to cDNA5, is similar but not identical in the genomes of two strains of ASV, and homologous sequences are present in the genomes of other avian leukosis-sarcoma viruses. By contrast, we find little or no complementarity between cDNA5, and the genomes of golden pheasant virus (subgroup G of avian leukosis-sarcoma virus), Moloney murine leukemia virus, and Moloney murine sarcoma virus. This pattern of homologies mirrors that found at the 3′termini of RNA tumor virus genomes. A nucleotide sequence complementary to most or all of cDNA5, occurs within the 3′-half, but not at the 3′-terminus, of the ASV genome; we suggest that this sequence may be a ribosome-binding site. cDNA5, constitutes the bulk (usually greater than 75%) of DNA synthesized under conventional conditions with detergent-activated virions. Consequently, the use of this DNA to analyze homologies among retrovirus genomes is of limited value.