When I analyze PCR in agarose gel , the water is contaminated with transgen DNA and the negative control is not contaminated with transgen DNA. if is the same water for all samples , which is the cause of this?
The positive samples has transgen DNA.
If your water is contaminated then everything is contaminated. If you aren't getting any "contaminated" bands in your negative control then it is likely you have some bigger problems. the contamination could be from anything, it could also be happening after you add the water. so instead of the water being contaminated something else is. The best thing to do is start over from scratch. All new stuff. Next time aliquot everything so you don't contaminate your stock.
If your water control is next to your positive control it is easy to get cross contamination. It is important to use plugged tips at all time for PCR. I assume you have also used a native gene PCR to check that your negative control is suitable for amplification and does not contain inhibitors. If it does include inhibitors then it may not show a product even if your water is contaminated with the transgene template.
How are you measure contamination? If you are running out your samples on an agarose gel, you may be over-loading or spilling from a neighboring well into your water control. First, run out another gel and space your samples every other well. If that's not your problem, then you should toss ALL of your reagents (water, primers, buffer, taq, all of it), clean your work area, autoclave tips/pipets/tubes and start over with all new supplies.
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