The question is "When you run the agarose gel, you get only a single sharp band; does this means that your pyrosequencing will be fine?"
OMG, I shouldn't have answered "Yes", but should be a firm "No" or just a more polite "Probably".
The issue here is, before subjecting a DNA sample for pyrosequencing, it needs to be denatured into single-stranded DNA after the PCR. And to get the biotinylated PCR product to become a single-stranded DNA, we need to captured or immobilized the biotinylated PCR product to sepharose beads, which will be then denatured and washed, and finally been released into a plate which contains the buffer that has all the other component (s) for pyrosequencing reaction.
Of course, without a good PCR product, you will not get any pyrosequencing result, but by having a good PCR product will not promise you to have a great pyrosequencing product or result as well, because as you can see, there are so many steps are taken place after PCR which could go wrong if you are not careful.
So, the answer to the question "When you run the agarose gel, you get only a single sharp band; does this means that your pyrosequencing will be fine?" should always be a firm "No".
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