Thankfully, another lab has sequenced the bacterial genome, so you know where on the bacterial chromosome the genes you are inte
rested in are located, as well as the DNA sequences before and after them. To remove the genes from the chromosome, you will use enzymes called restriction endonucleases that will cut the DNA strand at specific base sequences. This "digestion" will allow you to tailor the DNA fragment that you will be removing from the chromosome so that you may know where the cuts will be made and what additional DNA bases may come with the fragment containing the genes you are interested in.
The cuts are that are made by endonucleases have two outcome. Either they will be of sticky ends or blunt ends. Both of these ends come as a result of type of endonuclease that we are going to use.
There are also some extra sequence fragments that came additionally after cutting procedure. For example, the endonuclease EcoR1 cut the DNA fragments from 5' end that are sticky in nature and extra fragments of AATT hang up after cutting.
