I am working on Bacterial diversity, for which I need to sequence more than 1000 bacteria, it is very tedious to go through DNA isolation, extraction, visualization, amplification of 16S rRNA, and purification for sequencing in further. So, I wish to use a bypass way to directly obtain 16S rRNA amplicon for sequencing.
You could try performing the 16s touch down PCR on your bactrial sample, it would probably help you bypass the DNA extraction step as it works great as a colony PCR
If you have your isolates growing in liquid culture, you can often just add 1-2 uL of the culture to your PCR reaction in place of your DNA extract. If the isolates are growing on a plate, I would pick out a colony with a sterile toothpick and put it in some sterile water, vortex, and use the solution in place of the DNA extract. Your usual PCR program should be fine, except possibly the first step (see below). You can then purify the PCR product for sequencing as usual.
A couple of notes: you may need to adjust the initial denaturation step temperature/time to get the cells to lyse, and not all bacteria can be used for colony PCR, probably because they don't lyse well, or because they contain inhibitors. E. coli usually works great, but Agrobacterium doesn't, for instance.
Good luck!
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