I have been using different kits and heat lysis methods but the DNA yields are normally low , even when I run the PCR on those samples, there us normally a smear of RNA with no bands at all or sometimes when I get bands the spectrophotometer readings are not quite consistent
Kindly consult this article -
< Article An Improved DNA Extraction Method for Efficient and Quantita...
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You can try 3% CTAB. It works very effectively for all our dinoflagellate/diatom cultures. It takes a little longer than the kits but the yields are great.
No amount of testing of different kits/methods is going to improve the quality of your input ("shit in shit out"). Is the DNA fresh, or has it been preserved from fresh and the number of cell input is high, then to be honest most methods will give you what you need, obviously with a slight variation (this is also dependent on what your doing downstream). Personally CTAB with phenol chloroform is the best, but for a kit Qiagen DNeasy plant works well. If you're getting a smear then do an RNase treatment. Lots of papers explain these methods clearly for protist. Once you have DNA (in H2O or tris, EDTA is an inhibitor) run a Qubit to quantify and a gel to qualify. Is the DNA fragmented then you can forget PCR, especially if it is long range. If you have high weight DNA and you'r PCR isn't working then the problem isn't the DNA but an element in the PCR. The first guess being the primers, but that's a whole new question ;)
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