We are characterizing YADH-1 in my biochemistry lab course. Over the course of the first weeks, we harvested E. coli cells, and isolated plasmid DNA via alkaline cell lysis. A previous exam for the course asked the following question concerning plasmid DNA and analysis:
"Is chromosomal DNA more likely to interfere with restriction mapping, with PCR analysis, or equally likely to interfere with both methods?"
Since we're using EcoRI and BamHI, my thought process is that while we can predict the cuts on a circular plasmid, we wouldn't be able to predict all of the cuts on high-molecular weight chromosomal DNA, and the resulting restriction map would be useless. However, PCR can work in a complex mixture of molecules, so even in chromosomal DNA, the primers should be able to find the target sequence. Is the answer therefore that chromosomal DNA is more likely to interfere with restriction mapping?