Unspecific PCR bands - Why that happens? (Aug/25/2008 )

I've got some unspecific bands on the agarose gel right after PCR. My boss told me they might be contamination of any: samples, primers, enzyme... and so on.

Then another professor at another lab told the lab technician that we should discard used gels in another room because that might lead to contamination I usually discard my gels on the biohazard bin (that has a lid) but the lab tech insisted that I should use a big jar in the dark room that was placed by the other professor specially for that purpose. She was not able to explain me the logical basis of that. It sounds rather odd to me (gel drying and getting DNA in the air and blah blah...)

Is that accurate or someone here is making up some weird theory?

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You should try to run a gradient with your PCR to see which is the optimal annealing temp. with your primers. I doubt that it is contamination just because old gels are stored next to it.

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Agree.

Try to optimize the anealing temperature of the PCR run.

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I agree with them. optimize the annealing temperature. I guess the professor might have told different things. may be the contaminatin of EtBr used to visualize the gel. He may be concerend with the harm to human not with the experiments.

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I would say definitly ....(i) we are using used PCR plates that were cleaned in the dishwasher to mix PCR product and loading dye....no contamination there and this would be much more probable at least in my eyes!!!!!
(ii) some people in my lab reused old agarose gels for routine scanning of PCR...no more strange bands there than when using new gels!

so I would agree with your prof. and/or the former posters: either contamination or unspecific PCR!

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Thanks a lot for your advise! Actually, I optimized the annealing temperature and now it worked fine!!

Thanks!

Regarding the gel contamination... I will ask that professor in person. Probably the lab tech did not understand what he said exactly or I did not understand the lab tech...

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