Groove binding ligands for the interaction with parallel-stranded ps-duplex DNA and triplex DNA

DNA adopts different conformations not only based on novel base pairs, but also with different chain polarities. Besides several duplex structures (A, B, Z, parallel stranded (ps)-DNA, etc.), DNA also forms higher-order structures like triplex, tetraplex, and i-motif. Each of these structures has its own biological significance. The ps-duplexes have been found to be resistant to certain nucleases and endonucleases. Molecules that promote triple-helix formation have significant potential. These investigations have many therapeutic advantages which may be useful in the regulation of the expression of genes responsible for certain diseases by locking either their transcription (antigene) or translation (antisense). Each DNA minor groove binding ligand (MGBL) interacts with DNA through helical minor groove recognition in a sequence-specific manner, and this interferes with several DNA-associated processes. Incidentally, these ligands interact with some non-B-DNA and with higher-order DNA structures including ps-DNA and triplexes. While the design and recognition of minor grooves of duplex DNA by specific MGBLs have been a topic of many reports, limited information is available on the binding behavior of MGBLs with nonduplex DNA. In this review, we summarize various attempts of the interaction of MGBLs with ps-DNA and DNA triplexes.