I wonder if anybody has an experience of sequencing PCR products where master mix contains green dye for gel loading. What if I will purify them with enzymes instead of gel extraction or purification with columns?
while it might depend on the specific device / protocol, the use of dyes should generally be avoided in Sanger sequencing, as they will mess with the reading and can even damage the instrument calibration. At least this is what I've been told by Macrogen when asking them a similar question (about Taqman probes, in my case)
Please don't use master mixes which contain any kind of dye. It's not easy to get rid off these dyes before sequencing.
Macrogen support answered: "We do receive some samples with some dye mixed, and mostly the results are ok. Only if the dye is fluorescent, it would cause a problem." So, I will give a try and let you know about the result.
Hopefully, that works out well, if the green dye is not fluorescent. I will be waiting for your feedback.
What kind of green master mix it is and whether it contains a high fidelity polymerase? The purification of the PCR product is always desirable. If the dye is not fluorescent, it might be ok but not easy to get rid of before sequencing.
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