The functionality of CRISPR-based probes revolves around the use of the CRISPR-Cas system, particularly the Cas9 or dCas9 (dead Cas9) protein, which can be programmed to target specific DNA sequences. By fusing dCas9 with fluorescent proteins or other reporter molecules, researchers can create probes that bind to specific gene locations, allowing for real-time visualization of genetic elements within a tissue section.