We forgot a washing step during DNA extraction with 70% ethanol but washed it with 100% ethanol which was the next step, however PCR gave good bands at the expected size range. Will this salt remain during sequencing after purification of the PCR product? what problems can it cause?
If you have generated a pcr product then the salt has not only been diluted in the 100% ethanol wash but further diluted in the pcr reaction mix. It will have no effect on the sequencing reaction and most salts will be removed in the sequencing reaction clean up prior to running the sequence. There will be no measurable effect. Excess salt at the sample loading step of sequencing may cause slightly slower and lower loading in extreme cases but in your case it should not make any difference
there is special kits and protocoles to purify your PCR products
Washing the DNA with 100% ethanol instead of 70% ethanol doesn't matter after you have your PCR product - assuming that the DNA was only a small portion of the final reaction volume. Try your usual sequencing protocol and good luck!
Shouldn't be a problem since your PCR was successful. What are you using/doing for PCR purification?
There are kits that you can use to quickly clean up PCR products, such as the Column-Pure Gel and PCR Clean-Up Kit from abm. cat number: D516, or the QIAquick PCR Purification Kit Cat. No. / ID: 28104. Both works well for me, but abm is cheaper and does the job.
Alternatively, if you're sending your sample to a third party for sequencing, you can also ask them to perform the purification for a small additional cost.
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