Fluorescence in situ hybridization (FISH) is a molecular cytogenetic technique that enables the detection of specific DNA or RNA sequences on chromosomes and nuclei.
FISH is very important molecular technique not only in plant and animal research but also for clinical and medical applications such as tumor diagnosis and prognosis (1), chromosome aberration (2) and prenatal chromosomal analysis. The principle of this method is to hybridize small stranded nucleic acid such as DNA and RNA (probe) to complementary single sequences on chromosomes or nuclei (target), which are immobilized on glass slides. The probes are labeled directly or indirectly using e.g fluorescent nucleotides. These labeled nucleotides, which carry a covalent bond with a fluorochrome, are synthetically produced. When this fluorophore is exited with light of a specific wavelength meeting the characteristics of the molecule, it emits fluorescence, which can be detected under the microscope. The probes could also be indirectly labeled using molecules, which could be detected through fluorescent antibodies or in a radioactive manner (2).
After labelling FISH probes and targets are thermally denatured and hybridized. The standard FISH has, however, often some limitations, namely poor signal to background noise ratio due to nonspecific binding of probes to the chromosomes or cell surface. In addition the labeling rate of traditional FISH probes is low. Therefore, routine in situ detection of sequences requires highly labeled and sensitive probes, which are not always available.