Why does nature rely on RNA primer for the start of DNA Replication? Why not simply use DNA primer and make life simple !
1 Answer
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Biochemically none of the DNA-dependent DNA polymerases involved in DNA replication have the ability to begin elongation without a 5' to 3' primer.
The only DNA Polymerase that can catalyze elongation without a 5' to 3' primer is Reverse Transcriptase, however Reverse Transcriptase is an RNA-dependent DNA polymerase, and that accounts for the difference.
And if your next question is, but why, the answer is that that is how the systems evolved. Also DNA Polymerases have a much higher rate of fidelity due to error checking than RNA Polymerases do, and as the RNA primers get removed anyway and replaced with DNA, an error here or there in the primer will not matter.
The RNA-DNA duplex is also less stable than the DNA to DNA duplex, so it makes it easier for FEN1 to remove an RNA Primer than it would a DNA primer, assuming that the mechanism of primer removal and replacement after the complementary leading and lagging strands have been synthesized remained in place.
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$\begingroup$ Main reason is that DNA pol needs template while RNA pol does not. Hence DNA pol need initial primer (which is made by RNA pol or primase ). That is why there is RNA primer not DNA. $\endgroup$– DexterSep 23, 2015 at 19:40
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$\begingroup$ @Dexter Did you read my answer? "... none of... have the ability... without a 5' to 3' primer. Third paragraph addresses your 2nd point. $\endgroup$– AMRSep 23, 2015 at 19:43
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$\begingroup$ I am still unclear from your answer. You gave fact not reason. I think reason should be "need of template" as question was asked why RNA primer not DNA. And how is error correction is contributing to RNA primer not DNA ? I think, error correction is output not reason. $\endgroup$– DexterSep 23, 2015 at 19:49
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$\begingroup$ @Dexter The reason is that is how the system evolved. But as to make the answer little more than a comment, the reason DNA Polymerase needs any primer is the answer that addresses the first question, "Why does nature rely on RNA primer for the start of DNA Replication?" And the reason is that the DNA-directed DNA Polymerases involved in DNA replication do not have the ability to begin elongation without a 5' to 3' primer. That answers the first question. $\endgroup$– AMRSep 23, 2015 at 23:57
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$\begingroup$ @Dexter, I will concede I could have been clearer, but the basic thing I was getting at with the third paragraph is that DNA-directed RNA primers are sloppy replicators, but as the primer is removed and replaced, you can sustain errors in the primers without detriment to the organism. I would guess that the energetic cost of using RNA primers is less and it works faster than an equivalently abled DNA polymerase could in laying down a primer, which is why we have Primase as an RNA Polymerase and not a DNA Polymerase. $\endgroup$– AMRSep 24, 2015 at 0:02