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"CRISPR" and "Cas9" are different things. When a virus attacks a bacteria, the bacteria stores the viral code of the virus in CRISPR. And when the virus attacks again the Cas9 protein uses the RNA in the CRISPR to find the viral DNA and then destroy it.

So, what is the use of CRISPR when scientists use the CRISPR/Cas9 system to edit genes, as we have already given the Cas9 protein a guide RNA?

Sorry if this is a stupid question, I am new to genetic engineering and couldn't find the answer on google.

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  • $\begingroup$ I might be wrong here. But, when a virus attacks a bacteria, the bacteria stores the viral code of the virus in SPACERS and not CRISPR. 'Spacers' refer to the segments of DNA between the CRISPR. $\endgroup$
    – skpro19
    May 18, 2021 at 15:41

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Diagram of adaptive immunity mediated by CRISPR RNA, from https://sitn.hms.harvard.edu/flash/2014/crispr-a-game-changing-genetic-engineering-technique/ Figure 1. Process of bacterial immunity mediated by CRISPR/Cas9. Scissors are Cas9 enzyme, black diamonds are CRISPR elements in DNA.

As suggested in the comment, there are some subtle differences here. Cas9 knows where to cut based on the spacer (the colored squares). That serves as a guide to the enzyme through sequence complementarity of the transcribed spacer RNA in the crisprRNA (crRNA, shown as the squiggled black line with a green piece).

The crRNA itself is composed of the spacer and also a transcribed CRISPR repeat (black diamonds), which form the structural hairpin of the RNA molecule (the squiggly black piece) that allows Cas9 to recognize it as a crRNA. Otherwise the spacer would just be a random little piece of RNA floating around the cell; with a full mature crRNA Cas9 knows how to bind to both the crRNA and the spacer-defined target to do its cutting.

To directly answer your question then, the crRNA is the guide RNA. You have a CRISPR (or CRISPR-like) sequence already in there. It doesn't exist in the array named as CRISPR in bacteria, but the functional component allowing the enzyme to bind and then recognize the target exists in there.

It's a little more complex than that in the actual organisms, if you have more questions I recommend reading more on wikipedia.

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