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Recognition of DNA:RNA hybrid and triplex structures by a series of benzothiazole ligands

DNA:RNA hybrids and triplexes are formed as intermediate structures during many biologically important processes such as DNA replication, transcription, telomere replication and modulation of structure and/or function of specific genes (antigene strategy for gene regulation).[1, 2, 3, 4, ] Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (1-9) were screened by competition dialysis assay. The main aim of this study was detection of benzothiazole structure/s with preferential binding to DNA:RNA hybrids and ATT triplex in regard to regular (non-hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, screened by this method, were then characterised by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy and isothermal titration calorimetry. Compounds 1 and 6 showed the highest affinities toward 13 nucleic acid structures while 5, despite lower affinities, yielded higher selectivity among studied compounds. While both 6 and 1 exerted high binding affinities toward ATT, the latter showed stronger binding to rAdT hybrid whereas the former preferred dArU hybrid. Modes of binding to ATT triplex, dArU and rAdT hybrids were determined via CD spectroscopy.

ATT triplex, benzothiazole ligands, circular dichroism, hybrid DNA:RNA

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