I have purified my PCR product but after that I ran the gel and it showed double bands as shown in photo. what should I do. should I sent it for sequencing or not?
In the current form, it is very possible to get unsuitable sequencing results. Are you sure about the PCR conditions? Do you select the best thermal cycling program to amplify your gene-of-interest?
Have you blasted your primers? is it possible they bind other sequences? Are there other known isoforms for you PCR product, which may include/exclude certain exons?
Also make sure your primer stocks are clean (primer dimer, DNA pollution etc.)
Did you see two bands BEFORE you did the cleanup? If yes, then that's exactly what I'd expect to happen. The cleanup will remove unused dNTPs and primers and that's it.
Use a clean razor blade or scalpel to carefully cut out the band you want. You can always run the agarose gel for a longer time to get more distance separating the bands & less chance to accidentally include both.
Make the agarose cube as small as possible while still keeping all of the DNA band. Then, choose a purification method & send it off to sequence.
Looks like your primers are binding to something that isn't your target.
Either use a different primer pair or try to adjust the annealing temperature.
If that does not work, you can also run a purifying agarose gel with your entire PCR product, cut out the desired band, and extract the DNA from the gel (e.g. using a kit).
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