Hi, I have just bought a new 100bp DNA marker and I performed gel electrophoresis with 1.5% agarose gel stained with GelRed. Unfortunately the DNA marker was clumped in the middle with unclear separation.
I used different 100bp marker brand with EtBr staining before this and I was wondering whether different marker brand and stain require different 'treatment' in electrophoresis.
Should I try to use the new marker with EtBr or is there any other suggestion for me?
Thank you very much.
this is unusual these days. Long ago we used to have to heat ladders to 65c before running as sometimes the bands religated a littleat the cohesive ends but this no longer happens. I suspect either the agarose has not melted completely and the marker ran into a local area of high concentration agarose ( mix the agarose well after melting and check for lumps before pouring the gel). Or that it is essential that the loading conditions are very similar between samples and ladder in that glycerol and salt concentrations should be the same for the samples to run properly. If the ladder was in a small volume and high salt buffer that might cause it to run erratically or possibly even if the electrophoresis tank was on a slope and there was little buffer over the edge where you loaded the ladder the edge lane might run badly
Most of the DNA markers are similar in composition irrespective of brands,their duty is just to visualize whether the DNA or any samples travelling through the gel as most of the biological components are colorless,and making the sample sit in the well sometimes these also act as density gradients,if the marker composition is same in both the brands there will be no problem to carry out the experiment ,the bands appear based on the sample composition not on the marker used and bands appear due to staining which suitable staining can be used.
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