Question

Why is it that DNA polymerase requires a primer/ free 3' OH end to start elongation and RNA polymerase doesnt require it and starts de novo?

Answer 1

Actually, a limitation of the DNA polymerase III is that it cannot start synthesis of a new single DNA strand on its own. The function of the DNA polymerase III is to add a 5' phosphate of a free nucleotide to an existing 3' hydroxyl group (-OH). A primer, which is laid down by an RNA primase is an oligonucleotide, provides a free 3' hydroxyl group (-OH) which is perfect for the DNA polymerase III which synthesises DNA only in the 5' to 3' direction.

As far as RNA polymerase is concerned, it doesn't require a primer since it can recognize the first base of the transcriptional unit and lays down the complementary nucleotide accordingly. Hence, unlike the DNA polymerase III, a 3' hydroxyl group (-OH) is not needed which leads to no primers for the action of RNA polymerase.

Answer 2

To add on to what @Kayne said,

Is a DNA Polymerase enzyme that does not require a primer simply too complex for nature to produce? Probably not - consider DNA polymerase’s cousin, RNA polymerase, which can initiate synthesis of an mRNA strand de novo. So it is likely that such a DNA polymerase existed - however, as it has not been found in any organism yet, we can conclude that the cons of having such an enzyme far outweighed the pros.

Comparing RNA and DNA polymerase once more, we note that RNA polymerase has relatively limited proofreading abilities. This makes sense when we consider the millions of RNA strands that are transcribed - one faulty strand won’t make a big difference. In comparison, DNA polymerase must have exceptional proofreading abilities (1 x10^9 errors per nucleotide polymerized); errors in DNA are usually highly detrimental. We can hypothesize, then, that the ability to synthesize strands de novo and an enzyme’s proofreading ability are linked.

In other words, an enzyme (such as RNA polymerase) capable of synthesizing strands from scratch gives up some copying fidelity, while an enzyme (such as DNA polymerase) capable of proofreading gives up the ability to start a new strand.

Using this argument, we can also figure out why the primers for replication are made of RNA, instead of DNA. DNA primase shares characteristics similar to RNA polymerase - it has the ability to start synthesis anew; thus, it will likely have a higher error rate. If DNA primase used a primer comprising DNA nucleotides, the error-filled primer would then be incorporated into the genome.

To preserve genome integrity, a DNA primase that specifically uses RNA nucleotides has been selected for, as RNA is not incorporated into the genome. Thus, this RNA-using DNA primase can synthesize the necessary primer for the more accurate DNA polymerase to work off of, while at the same time ensuring its faulty primer is not incorporated into the genome. In later steps, the RNA primer is removed and replaced by DNA.

Answer 3

@kma 230- actually i asked why DNA polymerase is evolved to require a primer and RNA polymerase doesn't and as per your answer I deduce that this could be one of the ways to improve the proofreading ability of DNA polymerase. Now lets say I build a RNA polymerase which also acts on primer by taking the primer recognition domain from DNA polymerase can I say that the genetically engineered RNA polymerase will produce rna with less errors.If that so then why isn't that RNA polymerase designed to act on primers (the other way round of my first question).Then to answer this can I say is it beacuse it doesnt need to as the primer recognition might require expenditure of energy,is it?

Answer 4

or lets say is it beacuse RNA are unstable and are constantly made or destroyed.Thus cell doesnt worry much about the chances of occurrence of errors in RNA than DNA

Answer 5

I would say it's likely because of your second response - that RNA are unstable, and there's no selective pressure for such an RNA polymerase to have developed.

Unfortunately I don't have the time right now to search through the literature and find you some better answers, but great question! What do you think, @blues ?