tRNATrp as primer for RNA-directed DNA polymerase: structural determinants of function.

The specific interactions between the RNA-directed DNA polymerase of avian oncornavirus and the tRNATrp primer required for initiation of viral DNA synthesis in vitro were examined. Two distinct interactions, stable binding of the tRNATrp to the enzyme and initiation of viral DNA synthesis by the enzyme with tRNATrp as primer, were characterized as to the structure of tRNATrp required. Different structural features of the tRNATrp were shown to be necessary for each type of interaction. The entire primary structure and native conformation of tRNATrp are both required for binding to reverse transcriptase. Fragments of tRNATrp and intact tRNATrp in an altered conformation cannot be bound by the enzyme using an assay which detects high affinity binding between reverse transcriptase and native tRNATrp. In contrast, fragments of the tRNATrp molecule can serve as primers for viral DNA synthesis with normal efficiency as compared to intact tRNATrp. The fragments which initiate transcription must contain a minimum specific nucleotide sequence which extends from the 3' terminus of the tRNATrp through 27 residues of the molecule. This portion of the tRNATrp may be a major structural determinant of specificity in initiation.