Primer in relation to 5' end? (DNA Replication)

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student12
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Primer in relation to 5' end? (DNA Replication)

Post by student12 » Thu Jun 08, 2006 11:33 am

I have a question regarding the RNA primer becoming deatach after DNA replication.

The enzyme DNA polymerase is responsible for DNA synthesis by adding the correct nucleotides onto the primer in the direction 3' to 5' on the DNA template strand. However, after DNA synthesis, the primer is removed.

So how does the newly synthesised DNA strand consist of a 5' and 3' if the primer is removed? (becuase the primer is the one containing the phosphate group, thus the 5' end.)

oppox
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Post by oppox » Thu Jun 08, 2006 12:55 pm

well its not the that the primer is removed completly, its the excess of free primer that is removed.

Basicly the primers is a short piece complemantary to the DNA strand, it doesnt have any overhang with the DNA fragment later to be cut off or anything. Saying it attach at the 3' end means that it is complementary to the lets say the 20 last bases in the 3' end of the DNA strand not that it attach "outside" the DNA strand. The polymerase adds bases "after" the primer, incorporating it into the new strand that it synthesize.

here is a picture of it, its hard to describe without one.
The primer showned in red.
http://en.wikipedia.org/wiki/PCR

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LilKim
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Post by LilKim » Thu Jun 08, 2006 3:04 pm

I'm not sure if you meant to say DNA primer versus "RNA primer" for DNA replication?

I've never used an RNA primer (but i'd guess that some people do?).

But as far as DNA primers (oligos.) yes, your primer and your DNTP's actually BECOME the newly synthesized strand of DNA. So, theoretically... if your PCR cycles for too long... you'd end up running out of primers and DNTP.

hope this helps (not sure if it will?)
- KIM

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Post by 2810712 » Fri Jun 09, 2006 5:52 am

It's not just primer that has the phosphate at 5' , when the primer is cut off after the synthesis of DNA , its removed with his 5-phosphate [ P at 5C] & the other P which was attached at prime's 3C end remains attached to the DNA strand at its 5 end. So DNA is still 3'5' Ped
Note that a nucleatide unit is has only one P n0t both the Ps ...

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