I suggest you aliquot you primer stock and irradiate them under UV for 5 minute. Make sure there is small distance between the UV lamp and your sample. If you have a UV transilluminator, just leave the samples on it. This will neutralize any contaminating DNA. Alternatively, you can irradiate in the same way your PCR mix before you add the sample and the polymerase

As far as your primer stock being "useful" at this point, it is not. However, if it were my material, I would keep it for the purpose of allowing an inexperienced future-intern practice PCR.

Sorry I am not of much assistance in this case.

Are you sure the contamination is in your primer stocks? If so, discard them, what else – apart from the suggestion Michael made – would you do with them?

just dump it! what else u can do with it?

I would throw your stock out and order a new one.

Primers are cheap (20-25 bp primers from IDT cost only a few dollars), so it's probably not worth the effort and price of any extra materials to work around the contamination.

I agree, ordering new primer stock is the cheapest and fastest solution.

The only exception is if the primer are labelled.

It is advisable to keep primer stocks separate of everything else and take great care against contamination. Contaminated working stocks are no issue if there is uncontaminated stocks around.

I suggest you aliquot you primer stock and irradiate them under UV for 5 minute. Make sure there is small distance between the UV lamp and your sample. If you have a UV transilluminator, just leave the samples on it. This will neutralize any contaminating DNA. Alternatively, you can irradiate in the same way your PCR mix before you add the sample and the polymerase

Abdelhalim, this is interesting, I want to know more. How is it possible to selectively neutralize contaminating DNA by UV without affecting the primers? Is it because DNA is double stranded and primers are not? or there is more than that?

Hi Davis,

You can read about it in detail. This is because UV induces dimerization of T which makes the contaminating DNA not permissible for the polymerase reaction….It can affect also primers but it is not the same, as their concentration and also their sequence may not suffer much damage. In addition, they can still anneal to he template and do not inhibit the extension.... Anyway, it is a good and efficient way to decontaminate PCR reactions.

Primer stock should be handled carefully. Contamination of the stock means,,,, NO GO_AHEAD. You need to discard it and when you procure the new, make sufficient aliquots so that you don't face the problem again.

Just discard the contaminated primers, and handled carefully next time

Just google for UV primer (or whatever reagent for PCR) decontamination and you will find a bench of pubmed publications, some in very respectable journals or books where they have addressed systematically this issue. Remember, contamination could spark not only primers but other reagents as well. In most molecular biology labs, even the atmosphere can be full of DNA droplets such plasmids, PCR fragment, etc…I will not be surprised if I have already integrated in my genome some of them :) In my experience, since I learned it 10 years ago, it has always worked.

While the suggestion of using UV to remove contamination from primers is sound, I would recommend to avoid using a UV transilluminator that is used to routinely handle PCR products. The amount of amplified DNA surrounding the area will most likely result in additional cross-conatamination. The least expensive solution (your time is very expensive) is to re-order primers, and follow the recommendations of aliquoting given above to prevent future contamination of your primer stock.

Abdelhalim Boukaba sir this is really interesting all these days whenever i find my primer stock contaminated i would discard it and order for a new stock i ll try with your idea once thanks

Thank you all for your kind answers.

Of course the best way is to re-ordering but knowing ways to get rid of contamination sounds great too. Thank you Abdelhalim for your remedy. I'll go through it soon.

However, another way I have been advised is to centrifugation of primers before every use at 7500 rpm for 5 min to get DNA precipitated and then use primers gently from the top.

Better to discard the primer and work with new. This will save your time/reagent. Alternatively, 0.1 µm filter may reduce contamination with bacteria and similar microbes in case of microbial associated contamination.

Dear Faruku Bande,

The question was already answered by several others weeks ago. Moreover, a reduction of contamination with 0.1 µm filters is not the point...