Strand selections resulting from the combined template-independent DNA synthesis and clamp activities of HIV-1 reverse transcriptase.

The reverse transcriptase (RT) of HIV-1 has a non-templated addition (NTA) activity and can perform template switches with a very short (even two nucleotides) complementarity between the 3'-ends of the primer donor strand and the template acceptor strands. We have studied how the combination of several pivotal parameters can all lead to strand switches during DNA synthesis by HIV-1 RT. These include dNTP bias in the NTA step, the availability of acceptor strands with 3'-end sequences complementary to the de novo-generated primer tails and the stabilities of the clamped duplexes formed between these primer tails and the acceptor strands.