I am going to check my gRNA efficiency by in vitro digestion of DNA with Cas9. I read the protocol from NEB website but have some doubts regarding that. I want to know whether i should do in vitro transcription of my gRNA duplex stock then go for digestion analysis. Should I amplify the whole sequence of target DNA or just i should amplify for only target sequence? Because this will be the DNA template for my digestion analysis. Thanks.

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