Gels 'blobby' - (Jun/07/2011 )
I've been running a few different PCRs using plasmid DNA. When run on a gel, the bands are present (that is not the issue), but clarity is poor and all bands are a bit 'blobby'. For now, I am just testing ladders and this is not an issue. However, I want to use this PCR set up to be able to differentiate between fragments that are just a few bp apart - clearly if my bands continue to look like this, I won't be able to do so. Because the ladder looks the same as the bands, the issue is with running the gel rather than with the PCR itself.
I have used 1.5% and 2.0% agarose with TBE buffer with the same results. I have ranged the voltage from 60-80V and I have ensured that the buffer reservoir is full in all instances. I am not sure what is the next step I could take to resolve this issue.
Help would be appreciated,
Sorry but I'm not a native English speaker. I define your word "blobby" as "soft mass"
I took a ruler, I measured you "well" height and length. I measure the same with your "band"... I find it is the same...
In other words, is your "well size" that makes it so. you try to use a well size of "10mm x 1mm" (or 0.8mm), your resolution will be improved.
Many thanks, I tried today with a thicker gel and it was in fact a little clearer, but still left 'trails' along each well. I will keep trying. Thanks again!