Primer Stability Survey.

John R. McQuiston zje8 at cdc.gov
Thu Sep 30 12:01:19 EST 1999


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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