Complex FISH probes comprising large spans of genomic DNA always contain a high amount of dispersed repetitive sequences that hamper the visualization of the specific signal of interest. To overcome this problem, different approaches have been elaborated that depend on the type of experiment and the quality of the probe. A classical way to suppress repetitive sequences is to use unlabeled competitor DNA (sheared total genomic DNA or repeated sequence enriched DNA fractions). Here we present two protocols: the first one describes rapid COT DNA isolation and the peculiarities of its use in different FISH experiments, and the second is used for COT-free FISH with complex probes and is based on a special software tool for image enhancement.
