With certain cationic lipids the inclusion of antibiotic in the transfection medium can kill the cells and compete with the DNA for binding sites on the transfection reagent.

If you are constantly getting bacterial contamination you should troubleshoot why that is. Are your consumables clean, check water bath, aseptic technique etc. 

u can use anitbiotic like penicillin-streptomycin in you media..i don't see any problem with that..i always add antibiotic in the media never had problem with transfection efficiency..i do crispr too...i always got the modified clones..are you knocking out or down?

Hi Anuj, Just for the conceptual clarity, CRISPR/CAS9 system is to knockout (not to knockdown) the genes. 

As for antibiotics, as Can pointed out, having antibiotics in the culture medium during transfection can severely reduce the transfection efficiency. However, you can replace the medium with a fresh antibiotic-containing medium ~6h post-transfection. This should solve your problem. Having said that, it is generally not a good lab practice to add antibiotics to your growth medium, since it reflects that you are compensating your bad technique by supplementing medium with antibiotics. Therefore, I will strongly recommend you to figure out and eliminate the source of contamination. 

Thank you everyone you all have helped me to move my research forward.

its not a big deal if you will use antibiotic as i also use Kanamycin sometimes.

Dear Esteemed Colleague,

Thank you for your inquiry concerning the incorporation of antibiotics in your CRISPR transfection protocols and subsequent cell culture practices. The decision to use antibiotics in cell culture media, particularly in the context of CRISPR-based genetic engineering, necessitates a nuanced understanding of both its advantages and potential drawbacks.

The primary rationale for including antibiotics in cell culture media is to prevent bacterial contamination, ensuring the purity and viability of your cell cultures. This is especially pertinent in experiments involving transfection, where the introduction of foreign DNA into cells can be a vector for contamination if not meticulously controlled.

When integrating antibiotics into CRISPR transfection workflows, several outcomes and considerations must be anticipated:

In summary, while the use of antibiotics in CRISPR transfection and cell culture can be beneficial for selecting transfected cells and preventing bacterial contamination, it is essential to carefully consider the choice of antibiotic, its concentration, and the potential impacts on cell health and gene editing efficiency. Empirical optimization, guided by the specifics of your cell system and genetic engineering goals, will be key to maximizing the success of your experiments.

I trust this explanation provides a comprehensive overview of the considerations and potential outcomes associated with the use of antibiotics in your CRISPR experiments.

Best regards.

Take a look at this protocol list; it could assist in understanding and solving the problem.