Synthesis of First DNA Strand

At the ends of the viral RNA are domains that are essential for production of the dsDNA copy of the RNA genome. A direct repeat element called R, 15-230 nt in length depending on the virus, is present at the two ends of the RNA genome. At the 5’ end of the genome, a unique sequence element called U5 (70-220 nt long) is present immediately downstream of R, and at the 3’ end of the genome a unique element called U3 (230-1200 nt) is present immediately upstream of R. On completion of DNA synthesis, these elements give rise to direct repeats present at the ends of the viral DNA, called the long terminal repeats or LTRs, which have the sequence U3—U5.


Immediately 3’ of U5 is a primer binding site (PBS), where 18 nucleotides are exactly complementary to the 3’ end of a specific cellular tRNA. Each genomic RNA molecule has bound to it at PBS one molecule of the appropriate tRNA, which is used as a primer for DNA synthesis. The tRNA used depends on the virus, and several different tRNAs are known to be used by different viruses.


Reverse transcription begins by extending the primer tRNA through U5 and R, and stops when the end of the RNA genome is reached. The cDNA product, called the first strong stop DNA, is then transferred while still attached to the primer, from the 5’ end of the RNA to the 3’. It is unknown whether transfer is usually to the 3’ end of the same molecule, to the 3’ end of the second copy of the genome, or randomly to either copy of the RNA in the virus. This transfer uses the repeat element R at the 5’ end 3’ ends – the DNA copy detaches from R at the 5’ end and anneals to R at the 3’ end, so that only one copy of R is present in the DNA transcript. RNase H is presumably important for this. During reverse transcription, the RNA strand is destroyed by RNase H about 18 nt behind the transcription point. The degradation of the RNA strand during transcription of the DNA copy may encourage the jump to the other end. Other components of the particle may also be involved in the jump.


After the jump, reverse transcription resumes until the 5’ end of the RNA template is reached. Note that the RNA strand now at PBS because RNase H has degraded the RNA strand of the DNA/RNA hybrid (but not the RNA in PBS because this is an RNA-RNA duplex). This process results in the formation of what is called first-strand DNA or minus-strand DNA, because it is the antimessage sense.

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