The meaning of DAPI bands observed after C-banding and FISH procedures

Under specific technical conditions chromosome staining with 4′,6-diamidino-2-phenylindole (DAPI) permits characterization of heterochromatic regions as AT-rich (DAPI+) or AT-poor (DAPI−), especially when the chromosomes are counterstained with chromomycin A3 (CMA), which preferentially binds to GC-rich DNA. DAPI+ bands also often have been observed after C-banding or FISH. In these cases, however, it is not clear whether only AT-rich regions stain positively with DAPI or other heterochromatins with different base compositions also are stained. We evaluated the meaning of DAPI bands observed after C-banding and FISH using three plant species bearing different types of heterochromatin: DAPI+/CMA−, DAP−/CMA+ and DAPI0/CMA0 (neutral bands). Additional tests were performed using propidium iodide, a fluorochrome without preferential affinity for AT or GC. Our results indicate that AT-rich heterochromatin stains as DAPI+ bands after C-banding or FISH, but other kinds of heterochromatin also may be stained by DAPI.