I used Native PAGE to examine the DNA self-assembling nanostructures after annealing. I run my PAGE in a ice bath and 1X TAE was used as buffered system. The gel had been pre-electrophoresised when the samples were added. The gel was stained by EtBr solution after electrophoresis. However, obvious smears emerged in each lane (as shown in the attachment). How can I deal with the smears? Someone have told me that it was normal to have smears on Native PAGE.
Hello Lan
By the look of your DNA marker, electrophoresis condition seems to be fine. There might be 2 reasons for the smear: 1- Too much DNA is loaded 2-Your DNA is already degraded
I suggest to run an intact DNA next to your samples to see the effect of your annealing procedure on quality of DNA.
Regards,
Seems your DNA is overloaded, try to decrease the loading amount of DNA.
The DNA ladder looks good, so no change in electrophoresis condition is required.
It's a fairly common phenomenon. Native gels are never going to look as neat as denaturing gels. Also, your bands don't look that smeary compared to an average native gel published in literature.
However, when running native gels with DNA-containing samples, I always add heparin (both to the gel itself and to my samples) to avoid non-specific interactions that DNA might have with other components of the sample or the matrix of the gel itself. I usually use 10 micrograms per mililiter. This could improve your gel.
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