What is plasmid recombination and why is it a concern?
It is well documented that retroviral plasmid DNAs are inherently prone to recombination through the long terminal repeat (LTR) regions. Recombination appears to be exacerbated by MAGIC-ready bacterial strains containing F’ episome. Thus, you will receive clones in a non-MAGIC bacterial strain, DH10βpir116. The nature of the recombination in the pSM2c retroviral vector is thought to be an LTR to LTR recombination, resulting in a complete loss of the shRNA sequence as well as the chloramphenicol and the puromycin resistance genes. The recombinant product may contain oriT, the RK6γ origin, the kanamycin resistance gene, and a portion of the LTRs. Unfortunately, it appears that despite the loss of chloramphenicol resistance, you cannot use chloramphenicol to select against the recombinant since it resides in cells with a complete (non-recombined) plasmid. It is therefore critical to stringently adhere to recommended growth conditions when culturing viral vectors in E. coli in order to red
