Reasons for PCR failure....?

Mayumi Yagi myagi at
Mon Aug 5 11:30:28 EST 1996

Hi, Bill,

The one that took me the longest time to figure out had to do with a
residue left in the tubes after autoclaving.  Apparently the autoclave was
malfunctioning, leaving water (and some mysterious unknown stuff,
presumably from the water pipes or something) in the tubes, and the
student helper was simply leaving them in an incubator to dry afterwards.
So, depending on how much water was left, I would get tubes from the same
container that would work fine, and others that totally killed the PCR.
It was especially fun because at the time I was trying to optimize several
different primer pairs, and it got to the point where I couldn't get
duplicates set up at the same time and run on the same machine to give me
the same results.  Finally I realized that the tubes didn't seem to be
wetting evenly (crooked meniscus).  Once we got the autoclave fixed,
things seem to have settled down to more manageable levels.

 Hope this helps,

On 2 Aug 1996, Bill Burnett wrote:

> Hi gang...
> Okay, we've all been there....  One day the PCR's are great, next day
> they don't work.  You change everything, they still don't work.  You
> clean, polish and sterilise everything and they still don't work.  You
> try multiple different water sources, you try different batches of taq,
> you prepare them on ice, you prepare them at RT, you do hot start, you
> don't do hot start, you check your cycler, you don't wear aftershave,
> you make new templates, you use old templates that used to look great...
> And they still don't work.
> So what's the weirdest, wackiest reason you've ever come up with for
> them not working?
> At this point, after 2 months, I'll try *anything*.
> Help!!!
> B.
> ----------------------------------------------------------------------------
> Bill Burnett: bbur at
> Scottish Association for Marine Science
> P.O. Box 3, Oban, Argyll, PA34 4AD.

Mayumi Yagi, Ph.D.
Research (151)
Veterans Affairs Medical Center
1660 South Columbian Way
Seattle, WA 98108
Tel (206)762-1010, ext 1918
Fax (206)764-2598

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