Hi, we sometimes get this weird stains on the agarose gels. We tried re-making TAE buffer and agarose from scratch (after some experiments, we were quite sure it was the buffer), we obtained a good gel (without those stains) but then the stains appeared again. Did anyone ever had that problem before? How can we fix it? Any idea what it is?
PS: On the right-hand side of the picture (where the stain is bigger) there was no sample loaded.
your gel is obviously well melted and well mixed to disperse the ETBr since the samples are running evenly so on the basis of the swirling in the top right of the gel this may be a gel surface effect maybe caused by pouring the very hot gel in a cold room ( or putting it in a fridge to set) so the top surface is setting too fast. try less Et Br and letting the gel cool in the flask for a while before pouring the gel into the tray
I agree with Dr. Rutland about that. We used to let the gel cool before pouring in the tray. I always touch the flask to make sure it is not too hot before pouring the gel. Another thing I forgot to mention about Et Br; when I work my project in Winnipeg, my colleague used to add very little amount of Et Br in the tray to increase the visualization of the bands. I tried that and it seemed perfect.
Hi, thanks a lot for your responses. I think that might be it. We will let the agarose cool for longer before pouring it on the gel and see if we get better images. I don't think it's the Et Br concentration since we use the same bath as everyone else in the department and we are the only ones having this problem. Thanks again.
use a chilled buffer and less voltage, even you expect the same result, replace the agarose
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