Synthesis of the Second DNA Strand

The first-strand DNA produced in this way is the template for second-strand (plus-strand) DNA synthesis. The primer for second-strand is an RNA oligonucleotide, called the polypurine tract or PPT, positioned immediately 5’ of U3, PPT survives RNase H degradation and its 3’ terminus is exact; that is, the cleavages to produce it are precise. In addition to this precise primer for plus-strand synthesis, which defines the boundary of U3 and thus of the LTR, additional priming sites are used in some Retroviruses, such as HIV.


The PPT plus-strand primer is extended through U3, R, U5, and into the region of the primer tRNA, which is still attached to the first-strand DNA. The 18 nucleotides of the tRNA primer that are complementary to the PBS are copied, but further copying is thought to be blocked by a modified nucleotide in the tRNA that cannot be copied. The tRNA primer is then removed by RNase H and a second jump occurs. In the second jump, the nascent second-strand DNA is transferred to the other end of the template, using the PBS sequence, which is now present at the 3’ ends of both strands. Synthesis of both strands of DNA resumes and it becomes full length and double stranded. The resulting dsDNA is cleaned up, probably by cellular enzymes. In the full-length, linear ds copy of the genome, the LTR sequence U3-R-U5 has been formed at both ends of the DNA genome.


It is of interest that RT, like DNA polymerases, requires a primer to synthesize DNA, but unlike most DNA polymerases it can copy either DNA or RNA, given the appropriate primers. Thus, the enzyme differs from the RNA replicases of RNA viruses, which use other mechanisms for the initiation of RNA replication.

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