Avian retrovirus RNA-directed DNA synthesis: Transcription at the 5′ terminus of the viral genome and the functional role for the viral terminal redundancy

Abstract

The size and structure of DNA synthesized on 35 S RNA·tRNA trp template primer complexes in reconstructed reactions by the avian retrovirus RNA-directed DNA polymerase in vitro have been elucidated. Under standard enzymatic reaction conditions three major species of DNA are initiated on tRNA trp at the 5′ end of the viral genome. Two of these are single stranded in nature and exhibit lengths of 70 and 100 nucleotides. The third is hairpin in structure and is 185 nucleotides in length. A precursor-product relationship has been demonstrated between DNA 70, DNA 100, and the hairpin DNA 185 species. Furthermore, it appears that hairpin DNA 185 is formed during DNA synthesis rather than after DNA synthesis as a consequence of the intramolecular folding of complementary sequences present in the DNA 185 transcript. Finally, we present data indicating that, in addition to conversion of DNA 100 to hairpin DNA, the DNA 100 species can attach to the 3′ end of the viral genome presumably by base pairing with the terminally redundant sequences at the 3′ terminus to provide a primer for the continuation of DNA transcription at this end of the viral RNA. These data provide a functional role in proviral DNA synthesis for the terminally repeated genomic sequences.