Primer Stability Survey.

Raj m_ravi_gupta at yahoo.com
Thu Sep 30 23:16:47 EST 1999


Actually, my problem is that I have five sequences out of which I want
to amplify only 3 and the others should not get amplified. So what is
the general number of bases I should look for at 3' end so that they
match the required one's but not the unrequired one's.

In article <2CCB6CA5A8A5D211AFD700A0240AFD6C03150693 at MCDC-US-NEWS>,
  zje8 at cdc.gov (John R. McQuiston) wrote:
> You can have a 3' mismatch with Taq but it isn't very happy.  A T at
the 3'
> will have little effect.
> Kwok et al Nuc. Acids Res vol 18:999-1005 Talks extensively about
this.  Also
> Huang.. Nuc. Acids res. vol.20:4567-4573.
>
> John
>
> CDC Atlanta.
>
>  In article <2ac2591e.5a40c5a4 at usw-ex0102-011.remarq.com>,
> nicholas_theodorakis at urmc.rochester.edu says...
> >
> >In article <7suro1$b38$1 at nnrp1.deja.com>, Raj
> ><m_ravi_gupta at yahoo.com> wrote:
> >> Dear friends,
> >> I have a query for which I have received varied
> >> answers and hence am
> >> not able to conclude. I wanted to know that how many
> >> base mismatch at 3'
> >> end of a primer are allowed for the PCR to be
> >> uneffected. I hope all
> >> those who know it will be replying soon.
> >> Thanks in advance.
> >> Raj
> >> --
> >> The presence of conscience is presence of GOD.
> >> Sent via Deja.com http://www.deja.com/
> >> Before you buy.
> >
> >Are you using Taq or a proofreading polymerase? A
> >proofreadng polymerase should "correct" the mismatch (which
> >may or may not be what you want). With Taq, I was under the
> >impression that it would not use a 3' end mismatch at all,
> >but perhaps someone who has actually done it might wish to
> >comment here.
> >
> >Nick
> >
> >
> >
> >* Sent from RemarQ http://www.remarq.com The Internet's Discussion
Network *
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>

--
The presence of conscience is presence of GOD.


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Before you buy.



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