DNA replication

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Simon - 18 Nov 2006 23:01 GMT

Hi, Everyone!

In DNA replication, DNA pol 1 binds to the 3' end of Okazaki fragment
and displaces RNA primer by virtue of its 5' to 3' exonuclease
activity. Why can't DNA pol 1 bind to the 3' end of RNA primer and
displace Okazaki fragment (resynthesize it) by virtue of the same
exonuclease acivity?

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Bob - 19 Nov 2006 02:55 GMT

>Hi, Everyone!
>
[quoted text clipped - 3 lines]
>displace Okazaki fragment (resynthesize it) by virtue of the same
>exonuclease acivity?

Offhand... (please check the details)

I suspect that Pol I never has access to the 3' end of a primer.
Primer formation is pretty well integrated into the replication
complex.

However, if you really mean the 3' end of a primer that has already
been elongated (which is perhaps implied by the part of your statement
about displacing the Okazaki fragment)... then there is no 3' end of
primer, precisely because it has been extended.

You might also check whether Pol I can extend from an RNA primer. I
suspect it can.

bob

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Simon - 20 Nov 2006 01:00 GMT

Dear Bob:

The way I understood it, DNA pol 1 should prime off from Okazaki
fragment and replace RNA nucleotides of the primer with
deoxynucleotides. DNA pol 1 has 5' to 3' exonuclease activity which is
indiscriminate of deoxyNTPs or NTPs. Thus to prevent replacement of the
already synthesized Okazaki fragment, DNA pol 1 must have a way to
distinguish Okazaki fragment from RNA primer.

As far as I know, Klenow fragment is used in DNA sequencing because if
lacks 5' to 3' exonuclease activity. But RNA is not involved in DNA
sequencing. Thus, since 5' to 3' exonuclease activity of DNA pol 1 is
of concern, it must apply to DNA.

How does DNA pol 1 distinguish RNA primer from Okazaki fragment?

Best regards,

Simon Dexter

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Bob - 20 Nov 2006 04:59 GMT

>Dear Bob:
>
[quoted text clipped - 11 lines]
>
>How does DNA pol 1 distinguish RNA primer from Okazaki fragment?

Funny... My mind was wandering this evening, and I realized that I had
probably mis-interpreted your question. What you are really asking is
how/why the Pol knows when to stop doing its replacement.

Good question. Don't know. It certainly wasn't known just a few yr
ago. If it is known, the person most likely to know is Mike O'Donnell.
He has spent much time on the signals between processes in (E. coli)
replication. I suggest you run a search on his name. If you can find
a recent review article, that might be best.

I'll have a look, but you might beat me to it. (If you find a good
reference, post it! (No need to send me the article; just post the
ref.)

I would note that Pol I is not highly processive. But that would not
seem to be a sufficient answer to the Q.

best,

bob

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Simon - 21 Nov 2006 11:18 GMT

Today I asked my professor and he does not know either. I will try to
find out more about Mike O'Donnell and his work.

Thank You Bob.

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Natural Science Forum / Biology / Biology / November 2006

DNA replication