Do you know any well working kit for extraction of the PCR product cut out of agarose gel? I have two bands on a gel and I need to extract both separately... I tried in past with terrible results.
Most kits work equally badly and my advice would be to use any commercial kit and be very careful not to load more than the kit reccomendated amount. Do an extra wash once the dna is bound to the membrane and elute with hot (70c) water or TE left on the column for twice the recommended time. If you just need a small amoi=unt of amplimer for sequencing or cloning the "freeze and squeeze" old method works. Cut out the band in agarose and put into a tube. Freeze and thaw the sample in the tube 4 times then spin down for 10 mins at maximum speed. The supernatant contains just the amplimer and TBE/TAE running buffer from the electrophoresis
You can use this ready kit: https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/dna-clean-up/qiaquick-gel-extraction-kit
or https://www.neb.com/products/t1030-monarch-pcr-dna-cleanup-kit-5-ug#Product%20Information
I would recommend cutting out 4-5 bands (of the same template, up ~400mg of gel) and extracting as a single sample. The thinner the gel, the better. Warming up the elution buffer to ~50-60˚C makes a big difference. We have ~50% yield using ZymoClean Gel extraction. For separation of different targets, skip a few wells or use different gels to avoid contamination. Good luck!
Are your terrible results a consequence of very low DNA yields or high impurities?
If it is got to do with the amount of impurities purified along the DNA you can PCR purify the already gel-purified product, although DNA yield will go down, I find this step almost critical for downstream applications