multiplex- programme to screen oligos/combinations

Hi folks- have a look at this link for a free programme for testing whether you markers are good together (and whether they produce primer dimer and hairpins). Anyone embarking on multiplex or having problems currently should have a look at this. It is obvious that some markers just do not seem to work in multiplex and you may be able to screen these oligos/combinations out before you start (e.g. Carl Vangestel found that the program highlighted that the pigtail on one of his markers was the problem- by replacing it with non-pigtailed he managed to get it to work nicely). Alex Ball (+ others?) is using this so if you need a quick instruction ask him. 

http://www.cstl.nist.gov/div831/strbase/AutoDimerHomepage/AutoDimerProgramHomepage.htm 

 (AutoDimer: a screening tool for primer-dimer and hairpin structures.  Biotechniques. 2004 Aug;37(2):226-31)

One response to “multiplex- programme to screen oligos/combinations

  1. The primer design program PRIMER3 does these checks too so if you designed your primers using PRIMER3 and didnt add pigtails you should be safe (and probably dont need to recheck).

    But if you added a pigtail your (reverse) primer then yep, they do need rechecking using Autodimer.

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