The cutting is mostly specific (given you have a reasonable target sequence - a pure 'GGGGGGGGGGGGGG' sequence is just chemically problematic anyway). The cutt

The cutting is mostly specific (given you have a reasonable target sequence - a pure 'GGGGGGGGGGGGGG' sequence is just chemically problematic anyway). The cutting splits the DNA in half completely. It has to rejoin itself (by a not-well understood mechanism termed 'NHEJ'). This rejoining of the DNA is the kind of 'well it works (mostly, sometimes!)' part that is actively being better understood. Cas9 really has no relevance to this part of the process - unless it is used as a platform to attach DNA-repair machinery onto. Like in all things biology, concentration and time matter. So if you leave Cas9 on 24/7 at very high concentrations with nothing to do, it will go ahead and cut all over the place. The goal is now to bring to bear everything else we know about biological expression to put the Cas9 homing system in its place, only when it should be in place. We already know pretty good mechanisms to make sure Cas9 only turns on under certain conditions, at certain times, is inhibited under other conditions, is otherwise made even more specific. Those are engineering 'details' at this point. And by 'details' I mean you have a huge academic and corporate effort underway currently figuring out how most efficiently and most accurately control Cas9's function. Common results with a naive wild-type Cas9 (which we have moved on from in a lot of ways): (no change): ====== --> ====== (unhealed breakage): ====== --> === & === (forwards insert): ====== --> ===(insert)=== (backwards insert): ====== --> ===(tresni)=== (tandem insert): ====== --> ===(insert)(insert)(...)=== (off-target insert): ====== --> =(insert)===== (intermediate failure: ====== --> ===(insert) & === || .... There are also very powerful uses for Cas9 that do not cleave DNA at all. Sticking a gigantic 'BREAK()' command onto Cas9 (that cannot cut DNA) can be very useful where the natural break command has been lost.