Question

Cells use RNA strands to serve as primers. PCR techniques for amplifying DNA samples use pre-synthesized DNA primers. Explain why RNA primers are not used when replicating DNA fragments in vitro.

Answer 1

Inside the cell, at the time of replication RNA primer is used to start the replication as the DNA polymerase cannot start the replication de novo and it needs a free 3'OH to start with. When the replication is over, in case of prokaryotic cells the RNA primer is removed and is replaced by the dNTPs by the enzyme DNA polymerase I through a process known as nick translation (In case of eukaryotes the RNA primer is replaced by different enzyme) and the newly synthesized part is ligated with the DNA strand using the enzyme DNA ligase.

Now, you can understand that if you provide with DNA primer, you can nicely circumvent the primer replacing step and ligation step.

So, at the time of in vitro synthesis of DNA through the process PCR, DNA primer is used to get rid of the RNA primer replacing and new dNTPs incorporation step which makes the PCR less complicated.