how many roots and how long do we actually need? is it better to cut the roots into 1-2mm and grind it or just shake it? what's the optimum PCR concentration to get nice, distinct and intense bands?What's the best method to extract DNA of bacteria and fungi present in orchid roots?
Depending on your purpose, you don't need very many roots. I would grind the root very well, remove the pulp, and incubate the juice for a few days in a nutrient broth or streaked onto a plate. You don't need very much template DNA for a successful PCR.
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