how can I set the parameter

Emir Khatipov khatipovNO at NOuchicago.edu
Thu Oct 18 09:43:10 EST 2001


The lower the negative value, the more stable is the complex(dimer, etc.).
Minus energy is because you need to apply Energy to break the dimer. AB +
E -> A + B, or AB -> A + B - E. As far as I remember, when selecting primers
among those that form dimers, you should prefer the pair that has energy of
dimerization less than 1 kcal/mol. However, in my experience, it does not
really matter too much. You can generally adjust your PCR conditions (
temps, times, salts) so that even very bad primers as predicted by software
work. The most important parameter is melting temperature. The lower it is,
the better is a chance that your primers will work.
Emir

<ryan> wrote in message news:20011017072036.16505.qmail at ww02.jatek.com...
> hi,all,
>
>        When I designed pcr primer by Oligo6, I got a result that the most
> stable 3'-dimer: 2bp,-1.3kcal/mol. Is that ok? And how much for 3bp, 4bp
> dimer? why they put a -  in front of kcal/mol?
>
>        thanks
>
>
> <http://www.biowww.net/forum/read.php?f=1&i=4172&t=4172>
>





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