I am doing a quality control on plasmid I ordered from Addgene. I want to verify the size of the plasmids. This is the second quality control because the transformed cells pass the antibiotic resistance test.
The gel is an agarose gel at 1% and I did the miniprep with homemade solution, not a kit. The Nanodrop gave me normal results of purified DNA, I checked de 260/280 and 230/260.
I know I runned the gel I bit too long but that smear is as if I only had RNA, I cannot even see the band of the plasmid.
I think you have no plasmid DNA in any of your samples. Based on the 1kb ladder the gel looks like it ran ok. So either your cells did not transform correctly or more likely you just lost your plasmid DNA during the mini prep. I think the latter is most likely because without RNAse you should have lots of RNA in your mini preps and I don't see any.
There is nothing wrong with using homemade mini prep solutions (I've done thousands of mini preps using homemade solutions) but you do need to be sure they are made correctly and you know how to use them correctly.
I found the problem. The stock solution of Tris was at ph 10, thus the solution I had a wrong pH. Probably the alkalinity of the solution degraded the DNA
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