Upon loading of the Cas9 ribonucleoprotein particles (RNPs) onto the Region of Interest (ROI), cleavage takes place at the 5’ end of the target strand, while, most of the time, the Cas9 RNP remains bound at the PAM-distal end.

As a result, the end of the ROI becomes exposed and thus available for ligation with the sequencing adapter during library prep, whereas the Cas9-bound end is protected and unavailable for ligation.

More details are available here.