Question

What does RNA primase do in DNA replication?

I know it adds an RNA primer to the DNA at the origin, but I distinctly remember my professor saying that it comes in again and adds a second primer. I don't see it anywhere in my book or online... was he just mistaken? I think he was explaining it toward the end of class, so he may have rushed and slipped up.

Answer 1

DNA synthesis by the DNA polymerase III occurs only in the 5' --> 3' direction. During replication, there is a replication fork which is formed as shown in the diagram

Also, note that the DNA strands are anti-parallel. Therefore, in order to maintain the
5'-->3' polarity of the newly synthesized DNA strands while the fork moves in one direction, DNA synthesis is made in opposite directions on the two template strands.

The leading strand which is synthesized in the direction of the opening fork is synthesized continuously which implies that for that particular strand, the RNA primase needs to come down only once to lay a primer. However, as you can see on the diagram, for the lagging strand - the one strand which is synthesized away from the opening fork - cannot be synthesized continuously. Consider the following diagram:


As you see from the second diagram, for the lagging strand, DNA is synthesized towards the end of the template strand. Since DNA polymerase III cannot initiate DNA synthesis on its own, if the RNA primase doesn't come back to lay down another primer, the lagging strand would be left uncompleted and I leave you to ponder on the consequences of such a tragedy.

Anyway, the bottom line is that your professor is right, the RNA primase does come a second time to lay down another primer. Actually, it comes more than twice, until the replication is over. As a result, DNA on the 3' ---> 5' template strand is synthesized into fragments which is known as the Okazaki fragments which are eventually joined by DNA polymerase I and DNA ligase.