I want to knock out a gene from the genome of a bacteria by CRISPR/cpf1 mediated genome editing. In this, I have designed a sgRNA to cleave my cpf1 target with the 17bp upstream PAM sequence.
In the case of homology repair template design, I am planning to design a 600bp of upstream overhang and 500bp downstream overhang next to the gene of interest.
My question is, is it necessary to check my repair template should not contain any PAM sequence or cpf1 which leads to the cleave the plasmid too?