Variable PCR results - Ideas and Suggestions?

Tung Tran Duc Tuan plg-ttdt at
Tue Oct 28 09:22:01 EST 1997

In article <344cac3d.2019757 at>, jonesd at says...
>I have been having a problem with an RT-PCR for murine IL-6.  After
>optimization, which went well, I have been unable to obtain consistent
>results, even in the same run.  
>The PCR is done in a mix using 1.5 mM MgCl, 50mM KCl, 10mM Tris, 0.1%
>Triton X-100, .1% NP-40, .1% Gelatin, 0.25 mM each dNTP's, 5 U Taq
>(Promega) and primers in a volume of 50 microliters.  The cycle is 1
>min at 95, 1 minute at 55, and 1.5 minutes at 72 degrees, for 35
>cycles in a Stratagene RoboCycler.  
>The problem is that there is run-to-run inconsistency, with bands
>either appearing or not in the spleen cDNA, and within run
>inconsistency - I have run 4 samples using the same mix, and the same
>cDNA on the same run - and 1 shows a very nice band, 1 shows a fuzzy,
>indeterminate band, and the other two show nothing.  
>I am getting a bit desperate, trying to get this to work, so I'd
>really appreciate any help!  Thank you.
>Douglas Jones
>jonesd at 
>(remove NOSPAM to reply from USENET)

I have some suggestions:

Add about 5 % DMSO to the reaction mix to obtain an higher stringency.

Reduces the amount of Taq-polymerase to 1 U per reaction

Increases the concentration of MgCl2 to 2mM

Increases the extension steps duration to 2 min.

Use Touch-down PCR:

Use an relatively high annaeling temperature for the 6 firsts cycles, then 
lowering this temperature with succesive cycles to en annealing temperature of 
55 C over 15 cycles and keep this temperature for the reste of cycles.


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