Hinged-DNA (H-DNA) is a triple-stranded DNA in which single stranded [W?1] DNA binds to a B-form DNA. A DNA fragment that contains tracts of alternating purine and pyrimidine [(RY)n] sequences with symmetrically mirror repeat (MR) region is embedded in H-DNA (triplex). Hoogsteen bonds between Watson-Crick duplex purine strand and third strand through the major groove contribute to H-DNA conformation (Figure 2 & Table 1). Triplex is termed as ‘perfect’ if it does not contain any mismatched bp between Watson-Crick duplex purine strand and the third strand, but if there is a mismatch then it is referred as ‘imperfect’ triplex.
For the prediction of the H-DNA, a strategy to hunt for cruciform DNA has been employed (Schroth & Ho, 1995). In this method, they searched for mirror repeats (MRs) instead of inverted repeats that is[W?2] found in the cruciform to identify H-DNA motifs using the same criteria along with the additional rule: the sequence of the MR was 100% homopurine/homopyrimidine and was <80% (dA-dT)-rich. Moshey Gal and Gaddis created web-based programs TRACTS (Gal et al., 2003) and TFO (Gaddis et al., 2006), respectively. Those programs locate perfect triplex-forming oligonucleotides from target sequences of user defined[W?3] genes (already annotated). Those programs search for homopurine spread regions that are allowed to be occasionally interrupted by a pyrimidine but[W?4] the methods do not report for intronic[W?5] or intergenic region. While the above mentioned[W?6] methods are used for predicting the perfect[W?7] triplex-forming sequences, the methods for predicting the imperfect triplexes have been also[W?8] reported (Mergny et al., 1991; Roberts & Crothers, 1991; Xodo et al, 1993)[W?9] . Finally, a new mapping tool has been developed for annotating perfect and imperfect triplex-forming sequence (pTTS) in any region of human[W?10] genome (Jenjaroenpun & Kuznetsov, 2009). The criteria that allows[W?11] this tool to hunt for pTTS is as follows: (i) minimal[W?12] length of TTS is ?15 nt; (ii) minimal[W?13] guanine content is ?50%; (iii) the number of pyrimidine insertions could be ranged from 0 nt to 3 nt (Jenjaroenpun & Kuznetsov, 2009). To inspect the co-occurrence and co-localization of these pTTS with other important[W?14] genomic features, they integrated information of these pTTS into G4 dataset and several USCS genome browser (Zweig et al, 2008)[W?15] annotation tracks. In 2011 a new H-DNA mapping tool has been[W?16] developed, which devises dynamic programming to search for DNA instead of relying on simple identification of homopurine and homopyrimidine tracts (Lexa et al., 2011). First[W?17] they established the isomorphic groups of triplets by cluster analysis of local minimal[W?18] structures of the triplets, then they pick up structures which have passed the set threshold based on angles and distances between the atoms. These triplets are scored semi-empirically, a match score of 2 for canonical triplets, a score of 1 for less usual triplets, while all other combinations are scored as a mismatch.