During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?
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2 Answers
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DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The primase however is a typical RNA polymerase, capable of initiating polynucleotide synthesis de novo by positioning a complementary ribonucleoside 5'-triphosphate opposite its complementary DNA base. The primase makes an RNA primer that the DNA polymerase can then use for chain extension. The RNA primer is ultimately degraded and replaced by a DNA polymerase.
The rationale for this difference is that DNA polymerases have an active site that is geared towards proofreading and that primerless initiation would be an error-prone process. By having the primers 'tagged' by virtue of them being RNA, it is possible for the replication machinery to use them but then replace them with a high fidelity DNA copy of the template strand.
Edit in response to OP comment: Synthesis of the leading strand consists of extending an existing DNA. However the leading strand is also originally initiated, at the ori element, with an RNA primer. Once that first initiation event has taken place the synthesis of the leading strand is simply a process of extending that original primer.
Some viruses employ ingenious variations on this theme such as using tRNA primers , or proteins - see Wikipedia.
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$\begingroup$ so why doesn't DNA polymerase need RNA primer in leading strand? $\endgroup$– RafiqueCommented Dec 13, 2012 at 8:00
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$\begingroup$ OK.thanks a lot bro....i really appreciate for giving time to answer..:) $\endgroup$– RafiqueCommented Dec 13, 2012 at 8:22
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$\begingroup$ Well, if the answer is useful, you might consider giving it an upvote, or even possibly accepting it. Entirely up to you of course - before accepting might be worth waiting for a day or two in case a better answer comes along. $\endgroup$ Commented Dec 13, 2012 at 9:02
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$\begingroup$ well i tried many time to vote it..but i need 15 reputations. i have 11 now...so the first i will do when i get 15 reptutations is that i will vote this answer...:) $\endgroup$– RafiqueCommented Dec 13, 2012 at 10:01
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1$\begingroup$ "but then replace them with a high fidelity DNA copy of the template strand" - I would suggest adding that at the very end of eukaryote (linear) chromosomes, there will not be any way to replace the RNA primer with DNA and it will hence be removed along with the leftover sDNA end to which it was attached - resulting in telomere shortening. $\endgroup$– ArmatusCommented May 29, 2013 at 10:06
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In simple terms:
Function of the RNA primer: DNA polymerases need a double-stranded DNA region to which they can attach in order to begin copying the rest of the DNA strand. In order to provide this double-stranded attachment site, RNA primers are added by primase, an RNA polymerase which does not require such an attachment site itself.
When DNA replication starts, one primer is needed at the start of the leading strand. The lagging strand will need new primers regularly, and they mark the start of the stretches known as Okazaki fragments.
Why is RNA used instead of DNA?: Adding primers is an error-prone process, and DNA replication must copy the original strand with as high fidelity as possible. Using RNA for primers and then copying the original using DNA means that there is "memory" of which bits of the new strand were originally primers and hence more likely to contain errors (any RNA in the copy must have been primers). This allows removing them, in order to then replace them with proper high-fidelity DNA copies. When this happens, there is double-stranded DNA around the sites where primers were located, allowing DNA polymerases to attach there and fill in the gaps.
Aside from this, I would guess using RNA for priming may be more energy-efficient as RNA is more reactive than DNA.
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$\begingroup$ Can you elaborate on how the use of RNA primers plays a role in high fidelity? $\endgroup$– RamilCommented Oct 17, 2016 at 19:56
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3$\begingroup$ Presumably, when a polymerase attaches, the first few bases are quite error-prone (wobbly attachment to single-stranded DNA, proofreading at this point would risk the polymerase dropping off the strand). Once the first few bases are added, the resulting double-stranded region can provide more stable attachment and allow proofreading to function properly. When done, it would be better to know which bits of the resulting strand were the first few (error-prone) bases, so that they can be removed and re-done with proofreading. Using a different type of molecule for the primer makes that possible. $\endgroup$– ArmatusCommented Oct 18, 2016 at 9:17
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$\begingroup$ So basically, is the need for primer in replication because DNA polymerase requires double stranded region and this primer being RNA helps distinguish the first few bases added which are error-prone? $\endgroup$– RamilCommented Oct 18, 2016 at 18:14
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$\begingroup$ Rather: being able to distinguish the first bases is good, and one possibility for this is to use RNA for them and DNA for the rest. To implement that, the easiest is to have two polymerases, one which makes RNA and can attach to single strands, and one which makes DNA but can only attach to existing double-stranded regions. $\endgroup$– ArmatusCommented Oct 19, 2016 at 12:07