Characterization of dna complementary to nucleotide sequences adjacent to poly(A) at the 3′-terminus of the avian sarcoma virus genome

We have prepared DNA complementary to a sequence of 300-400 nucleotides adjacent to the poly(A) at the 3′-terminus of the genome of avian sarcoma virus (ASV) DNA was transcribed from denatured ASV RNA following initiation on the primer (dT)_12-18. We demonstrated that homopolymer synthesis was not a significant feature of our enzymatic reaction, and we proved that most if not all the initiations on (dT)_12-18 occurred at or near the 3'-terminus of the viral RNA. The presence of oligo(dT) on cDNA₃, accelerates hybridization between cDNA₃, and polyadenylated viral RNA; this artifact can be eliminated by including a competing homopolymer [poly(dT) or poly(A)l in the reaction mixtures. Nucleotide sequences complementary to cDNA₃, occur only once or twice in the genome of avian sarcoma viruses, are present in the genomes of virus strains from subgroups A, B, C, D, E, and F of avian leukosis-sarcoma viruses, and are conserved even when large deletions affect an adjacent viral gene (src) By contrast, we find little or no complementarity between cDNA₃, and the genomes of golden pheasant virus (subgroup G of avian leukosis-sarcoma viruses), mouse mammary tumor virus, and the Moloney strains of murine sarcoma virus and murine leukemia virus. cDNA₃, can be used to identify the 3′-terminus of the avian sarcoma virus genome by molecular hybridization and will therefore be a useful reagent for the analysis of viral replication.