"How can I design an experiment using CRISPR/Cas9

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Ok, you want to use CRISPR/Cas9. I understand completely. But first, ask yourself why you want to use this "technology." Is it really the best method for achieving your desired end result? Remember, at its core, Cas9 is an enzyme which creates targeted double-stranded DNA breaks at specific locations within a double-stranded piece of DNA, which you can decide based on a 20nt gRNA molecule. If you are doing genetics in bacteria, ask yourself how this application (creating double stranded breaks when a specific sequence of 20nt is recognized) helps your project.

Cas9 is undoubtedly an incredibly useful tool in genetic engineering, but its primary purpose in E. coli is as a selection tool for experiments involving chromosomal changes by homologous recombination. It is certainly a very powerful selection tool, and a hot topic in current discussions regarding science and biotech, but understand its limitations before dedicating yourself to using Cas9 as a tool in your experiment. You may be able to arrive at your desired end result in a much faster way using more traditional techniques.

If you are doing chromosomal alterations in non-model bacterial species or eukaryotic chromosomal genetic manipulation, Cas9 may very likely be the cheapest, fastest, and easiest method to achieve your desired end result. If you are trying to design regulatory proteins that bind DNA of interest using modified Cas9, or perhaps have applications for targetted single strand breaks, again modified (though a different modification) Cas9 could be perfect for you! Don't be discouraged by my words, just think critically about WHY you want to use CRISPR/Cas9. If, in the end, you want to use it just because its cool, well that's okay too! After all, science is cool!

Good luck :)