This seems like perhaps the wrong place to ask this, but maybe asking on a site directed towards school children would give me a more clear, basic answer. This is a laboratory technique question.
I am a molecular biology tech, as of 2 weeks ago. I have spent less than ten days doing these techniques, and I am concerned about one thing in particular that I'd like to "nip in the bud" as soon as I can. After doing a few minipreps and subsequent restriction digests, my gels have shown what looks like gradually more and more supercoiled and nicked plasmid, gradually less linearized plasmid, and none of the desired insert.
I was wondering if high amounts of supercoiled and nicked plasmid is a sign of bad technique during the miniprep or is it a problem from something previous/upstream like the ligation or the transformation?
PS. I have attached pictures of some of my gels, in chronological order. The dates are in the file name. As you can see, they get uglier and uglier. Note: the negative control is the first sample on the bottom row next to the ladder/size marker.