I have tried already Qiagen, Sigma and Thermo kits. Getting OK quality but low quantity… CTAP also was not good. I need at least 3 µg of concentration 50-100ng/µl. Would be greatful for all suggestions.
Have you thought/tried using DNA vacuum concentrator (CentriVap) instrument to concentrate the DNA first and then dissolve in appropriate buffer to achieve the required concentration? I guess this would work.
I worked with some difficult plant material, and found that low temperature all the way greatly increases DNA extraction efficiency. I used CTAB protocol with some changes, with following tweaks: grind tissue in pre-chilled mortars (-80 C; liquid nitrogen will go as well), all spinning in the cooling centrifuge (4 C), and keep sample tubes on ice between every step. Final DNA yield was usually very good even from partially damaged leaves.
And the best for you is to search existing literature. Arabidopsis is so popular model object, and there must exist perfectly optimized protocols.
You probably used DNeasy plant mini kit (Qiagen). When I eluated the DNA out of the column, I let it stand for a longer time than the instruction suggests. In an experiment we need larger quantity (ex. Southern for tobacco), I used CTAB method.
By the way, If you don't have many samples to do, they also have DNeasy plant max kit (Qiagen). I saw you have tried several different kits. The cost can be used to try a DNeasy plant max kit.
Mini: 50 column, $236
Max: 24 column, $380.
Do an "old-school" phenol-chloroform extraction. Remember, less is more when it comes to the amount of starting material. Use a piece of leaf the size of a pencil eraser. Store your samples in screw-cap vials in the -80* for really long-term storage.
Good luck!
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