Hi!
I am unable to differentiate these 3 fragments in an agarose gel. More concentrated agarose gels are working for lower size bands...
Some suggerences? Thank you in advance.
If these bands are related find a common restriction enzyme cut site, cut and separate 300, 200 and 225bp for example where the small fragments separate better on a2percent agarose. Alternatively redesign one primer so the amplified fragments are small and separate in high percentage gel.
run the gel slowly and in a cold room to minimise thermal diffusion
I think David is right: it depends what your goal is! Please explain what the fragments are and what, if anything, you intend to do with them.
Thank you for all your answers!
In fact we want to sequence the bands... Finally running agarose 2% gels overnight at 50V we've been able to separate the fragments. Bands obtained are quite weak... we'll try to do a PCR from DNA purified from these bands to obtain more DNA to be able to send a good amount to sequence.
Thank you again!
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