plasmid isolation - sth lights up in the well of agarose gel (Apr/06/2011 )
I have a problem with my plasmid isolation. I isolated a 9kb plasmid using a commercial kit. Then i checked my isolate on 1.2 % agarose gel. I ran the gel at 90 V for about 40 min.. I could see my plasmid as two bands but also there was sth stucked in the wells, lights up uner UV. I extended the runtime, after 67 min it was still there, If it is genomic DNA shuldnt it enter the gel after that long runtime..if it is not genomic DNA then wht can it be.. Any help appreciated! Thanks,
Genomic DNA will just stay at the down side of the well, not migrating. Likely your prep is not separating gDNA from plasmid DNA. Vortexing the lysed cells is a common problem -- use gentle mixing of the lysing solution.
I once had stuff stuck in the wells but I think it was because I had beads left in my DNA from a Qiagen gel extraction kit