Combinatorial selection of short triplex forming oligonucleotides for fluorescence in situ hybridisation COMBO-FISH

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“…The selection of an appropriate COMBO-FISH probe set [40] is the prerequisite of any COMBO-FISH experiment, be it a special and single research experiment or a standard application. In any case, the genomic area to be labeled has to be identified in the genomic data base and the corresponding sequence has to be extracted.…”

Selection of COMBO-FISH Probes for Multi-Purpose Applications

“…This method is called Combinatorial Oligo Fluorescence In Situ Hybridisation (COMBO-FISH) [10]. It can be used as well with the described TFOs as with common double-strand forming probes (Watson-Crick binding probes) both composed of DNA or peptide nucleic acids (PNAs) [10,11,12]. Schmitt et al have described the algorithms for designing such TFO-probes in ref.…”

“…Schmitt et al have described the algorithms for designing such TFO-probes in ref. [12]. By now this algorithm can also be used to identify and design Watson-Crick-binding probes [13].…”

“…As parameters for this search a minimum and a maximum length of the oligonucleotides, the number of probes determined and the maximum cluster size of probes which are allowed to bind within a sequence of selectable length outside the labelling site are to be defined. The algorithms Schmitt et al [12] created can be used as well on the genomic sequence database of the human genome as provided by the NCBI [14] as on a self-created database including the TFO-binding sites only.…”

“…Diversity of COMBO-FISH has shown that it is possible to create specific probes for a large amount of chromatin regions [12] in the range of some hundreds base-pairs up to the whole genome. On top studies showed that probes can not only be designed for the human genome but also for many other sequenced genomes [16].…”