Why doesn't PCR shorten DNA by-products?

[K Niner]

Note: Question at bottom in blue.

In DNA replication the DNA polymerase reads the template strand 3'->5' (or synthesizes the new DNA strand 5'->3', whichever you prefer) starting after the primer. But at the very end of the lagging strand the final okazaki fragment either 1) can't be primed (due to the primer sequence not being the absolute last DNA bases of the end of the strand) or 2) the terminal primer can't be converted into DNA (b/c the typical DNA polymerases add DNA after the primer, and the DNA polymerases that replace the primer with DNA nucleotides require a 3' strand extending beyond the primer, which obviously is not present).

To remedy this, Eukaryotes have telomeres, telomerase, etc. to prevent the shortening of the DNA strands. Prokaryotes have ciruclar DNA that doesn't have this problem.

All the above to understand where I'm coming from: Why, in PCR, are the target strands of successive DNA replications not shortened? What am I missing in the PCR mechanism?

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[TieuBachHo]

Note: Question at bottom in blue.

In DNA replication the DNA polymerase reads the template strand 3'->5' (or synthesizes the new DNA strand 5'->3', whichever you prefer) starting after the primer. But at the very end of the lagging strand the final okazaki fragment either 1) can't be primed (due to the primer sequence not being the absolute last DNA bases of the end of the strand) or 2) the terminal primer can't be converted into DNA (b/c the typical DNA polymerases add DNA after the primer, and the DNA polymerases that replace the primer with DNA nucleotides require a 3' strand extending beyond the primer, which obviously is not present).

To remedy this, Eukaryotes have telomeres, telomerase, etc. to prevent the shortening of the DNA strands. Prokaryotes have ciruclar DNA that doesn't have this problem.

All the above to understand where I'm coming from: Why, in PCR, are the target strands of successive DNA replications not shortened? What am I missing in the PCR mechanism?

I think you should ask this in Q&A?
PCR technique doesn't have a lagging strand.

 

[Medicalbound10]

If my memory serves me correct, after the two strands separate and are available to be copied, the primer is is there so that it can signal the specfic DNA of interest to be copied. Once the primer is there, the Taq polymerease ( DNA polymerease cousin) makes the copy ( let's say 5' to 3' until it runs into the end. While on the other strand, the primer is placed in the opposite side so that it runs 3'- 5' to the end. After 4 cycles or so only the strand of interest remain and the same section is amplified.

Hope it helps

 

[K Niner]

If my memory serves me correct, after the two strands separate and are available to be copied, the primer is is there so that it can signal the specfic DNA of interest to be copied. Once the primer is there, the Taq polymerease ( DNA polymerease cousin) makes the copy ( let's say 5' to 3' until it runs into the end. While on the other strand, the primer is placed in the opposite side so that it runs 3'- 5' to the end. After 4 cycles or so only the strand of interest remain and the same section is amplified.

Hope it helps

The DNA is copied by the Taq polymerase from the end of the primer forward, how is the DNA copied where the primer is bound?


@TieuBachHo, yeah I should have posted this in the Q&A section, my bad. I didn't realize ya'll had a seperate section for that.

 

[Drexon]

The DNA is copied by the Taq polymerase from the end of the primer forward, how is the DNA copied where the primer is bound?

It doesn't get copied by Taq polymerase. I'm having a hard trouble drawing the products of PCR amplification (hence the editing ) But ya you ask a valid question. The primer portion of the PCR amplification doesn't get amplified at all.

 

[K Niner]

It doesn't get copied by Taq polymerase. I'm having a hard trouble drawing the products of PCR amplification (hence the editing ) But ya you ask a valid question. The primer portion of the PCR amplification doesn't get amplified at all.

What I don't understand then is if the DNA that binds the primers isn't copied, how do the primers bind to the newly created strands on the next round of replication?

 

[Drexon]

What I don't understand then is if the DNA that binds the primers isn't copied, how do the primers bind to the newly created strands on the next round of replication?

Even though the primers aren't copied, they are incorporated into the newly synth DNA piece. Primers bind to DNA and Taq starts to synth DNA from the primer in a 5-3' manner. The newly synth piece of DNA actually incorporates the primer. I hope this makes sense.

 

[BHaus9]

http://en.wikipedia.org/wiki/Telomere#Telomere_shortening

Good -- and hopefully accurate -- explanation of telomeric shortening and why it occurs only in the lagging strand in eukaryotic replication (since both primers move in the 5' --> 3' direction in PCR, there is no lagging strand)

 

[SN2ed]

Thread moved. These types of questions belong in the Study Q&A forum.

 

[Riberiusz]

I know it's really old topic but I encountered today the same problem and that's probably the only site on Internet where it was mentioned. I even created an account here just to answer it to help the others, because I think the previous answers are not clear enough.
For leading strand during replication, primer is also needed, but only one at the start. Nevertheless, at the end, number of primers doesn't change the fact that both template strands become shorter at 3' ends (concerning lagging strand, only that at very 3' end is not replaced by nucliotides). Later, after replication, also amplified fragments are shorter, but at 5' ends (in comparison to template ones).
However, when it comes to PCR reaction, by-products indeed remain the same length. @Drexon is rigth, primers are incorporated to amplified fragment. It's all because they're short DNA fragments (not RNA, like in a case of replication inside a cell). Under normal conditions, eucaryotic cells are not able to produce free, short fragments of DNA which could serve as the ideal primers so they need to use RNA which can't be incorporated to amplified fragment.
I hope it will help someone

 

[aldol16]

There's both a forward primer and a reverse primer with PCR. So basically for PCR, the first you thing you have to do is denature the DNA into two separate strands. You're only amplifying one sequence, on one strand. You're going to design a forward primer and a reverse primer that flanks the region you're trying to amplify. With both forward and reverse primers in there, that's how you get amplification of the middle part. There are no ends involved.

 

[JustinM88]

Even though the primers aren't copied, they are incorporated into the newly synth DNA piece. Primers bind to DNA and Taq starts to synth DNA from the primer in a 5-3' manner. The newly synth piece of DNA actually incorporates the primer. I hope this makes sense.

Oh wow, I never thought about this before. The Primers are DNA primers (meaning, actually made of DNA rather than RNA), right? So this would actually make sense lol