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Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand in its major groove. This sequence-specific process offers a potent mechanism for targeting genomic loci of interest, that is of great interest for bio-technological and gene-therapeutic applications.
Triplex-formation requires a duplex, presumably DNA, and a single-stranded nucleotide sequence acting as the third strand, presumably RNA.
The process of predicting putative triplexes in sequence data can be divided into three steps:
identifying the triplex-forming oligonucleotides (TFO) in single-stranded sequences
identifying the triplex target sites in double-stranded sequences able to accomondate a third strand
assessing the compatibility of potential TFO/TTS pairs according to the canonical triplex formation rules
Triplexator, short for triple-helix locator, employs approximate pattern matching based on the triplex
