Primer requirement in DNA Replication

DNA Replication

DNA replication is required for copying the genetic material which inherited in daughter cells. The process of replication is an enzyme-dependent catalytic reaction, utilizing many proteins to do so. Primers in molecular biology are used to DNA synthesis as well as in PCR.

General Mechanism

DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP for DNA amplification in replication or PCR. The primase however is one type of RNA polymerase, capable of initiating polynucleotide synthesis de novo by positioning a complementary 7-10 long ribonucleoside 5'-triphosphate opposite its complementary to DNA base during replication. The primase makes an RNA primer that the DNA polymerase can then use for chain extension by adding dNTPs. The RNA primer is ultimately degraded and replaced with dNTPs by a DNA polymerase.

Now major questions come that why use energy for RNA degradation?

Why during evolution such a system opted?

A possible mechanism that DNA primer would work fine chemically, but the machine we have in the cell is an RNA polymerase more precisely primase.

On the other hand, if there was a DNA version of “primase”, then it would have to be capable of initiating a chain which would mean that it would have the same trade-off in terms of loss-of-accuracy. Because a starter polymerase must be more helpful to the first nucleotide it is adding than is healthy for good checking off the most recently added nucleotide. While such a DNA polymerase is perfectly possible, this would create a huge problem in that each DNA strand on the lagging strand would have its starter piece made by an incorrect (or rather, less accurate) DNA polymerase, but that region would be DNA just like the rest of the strand. So, there would be no signal of where the wrong primer ended, and the accurate continuation began. By using a slightly different molecule such as RNA as the primer, the system can check which parts must be erased and replaced using the proofreading activity of Polymerase as the Okazaki fragments are joined.

To understand this in simple words we can say that the rationale for this difference is that DNA polymerases have an active site that is geared towards proofreading and that primer-less initiation would be an error-prone process. By having the primers tagged by being RNA (as a primer), it is possible for the replication machinery to use them but then replace them with a high-fidelity DNA copy of the template strand.

One advantage of using an RNA primer (that is made somewhat inaccurately) is that it can later be easily recognized and itself replaced.

During PCR, we artificially prime the system using DNA primers.