FokI is used to cleave between any two base pairs. See Podhajska, A.J., Szybalski, W. (1985). Gene 40: 175-182 In brief, you synthesize an oligonucleotide which contains a double-stranded FokI site and a single-stranded extension which anneals to the DNA template at the point where you would like to cut. Anneal the oligonucleotide duplex to the single stranded DNA template. In the subsequent cleavage reaction, the FokI will bind to the double-stranded site on teh oligonucleotide duplex, and will cut the template to which it is annealed.
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