I intend to implement the method in Schuelke et al. (2000) to characterize microsatellite primers in different plant species at a lower cost. Schuelke used the M13(-21): TGTAAAACGACGGCCAGT, but I have seen that other authors used other universal primers, like ;M13 Reverse (-27): GGAAACAGCTATGACCA.
Is there any difference in peak quality or PCR yield using the different universal primers?
For multiIs it more appropriate to use the same universal primer tagged with different fluorophores, or to use a different primer for each fluorophore?
Hi Priscila...
I prefer M13 (-21), but you may use both of them for more accuracy! Different primers will be helpful more than different fluorophores!
Best luck.
Thank you Ayoob! But reading a bit more.... We decided to use the universal primers in Blacket et al. (2012). They have being used in plants already, and the PCR yield seems to be higher than with M13, with higher annealing temperatures.
Also, if you combine 4 different primer with 4 fluorophores, it allows you to multiplex in PCR and also for capillary electrophoresis.
I hope it works well... it will be our first approach with that technique.
All the best.
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