Molecular analysis of the second template switch during reverse transcription of the HIV RNA template

The molecular events leading to the second template switch during reverse transcription of the HIV genome were studied in a defined in-vitro system. In order to investigate displacement of the tRNA(lys) primer from the primer binding site (PBS) of the viral genomic RNA, following DIVA synthesis, we produced an HIV RNA/DNA substrate that resembles the intermediate reverse transcription complex formed prior to the second template switch. Partial tRNA(lys) primer displacement was observed during plus (+) strand DNA synthesis and during minus (-) strand DNA elongation. We found two determinants that may serve as a stop signal for (+) DNA strong stop synthesis, the A(m) at position 19 of the natural tRNA(lys) and the secondary structure at the PBS sequence. The later signal appears to constitute a stronger terminator in-vitro. The 3' end of the nascent (-) DNA strand prior to the second template switch was also determined. It was mapped to the US-PBS junction at the site for the first endonucleolytic cut introduced by the RNase H activity of the HIV reverse transcriptase (RT). Thus, different signals dictate the arrest of (-) and (+) nascent DNA synthesis. These stop signals appear to be required for the subsequent second template switch. However, an excess of (-) DNA ''acceptor'' molecules, having a 18-base sequence complementary to the (+) DNA ''donor'' template, was required to demonstrate the actual template switch in the in-vitro system. Taken together these results indicate that the reverse transcriptase can catalyze all the steps leading to the second template switch and auxiliary viral proteins may act to enhance the efficiency of this step during the reverse transcription process.