I would like to separate two DNA fragments obtained after a multiplex PCR which are 193 and 200 bp. Even with 3% agarose at 100V for 50 minutes it didn't work. Do you have any suggestion? I can't use PAGE or Metaphor agarose.
I have always had luck using a mixture of 3% low melting point agarose, and 1% regular agarose in TAE buffer. To save a few dollars, you can soak the used gel in fresh TAE buffer (for an hour or two), remove it from the buffer, re-melt it, and pour another gel. We have re-used agarose 3-5 times like this.
Thanks you David for your answer, I will try that but I did try a combinaison of 2% low melting and 1% regualr agarose but it didn't work. How long did you run your 4% gel and at what voltage? Thanks you
I am sorry Stephane I don't understand your comment.
I do not recall the exact times and voltages, and it depends on the thickness/length of your gel, and the ionic strength of your running buffer. As a general guideline, treat it as you would treat a regular agarose gel. If your bromophenol blue marker appears to be migrating too slow, increase the voltage, but don't let the gel get too hot. Since you are trying to separate fragments that are very close together, here are some tips to increase resolution: 1) run a long gel--10 cm in length or longer to get your bands to separate. 2) run a thinner gel (0.5 cm thick) and use thin combs (1.5 mm thickness). You will need to load more concentrated DNA, because the thinner combs will hold less volume, but it is easy to concentrate your DNA and get quantitative recovery with etOH precipitation.