Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands.

Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines-group 1, 2-thienyl/2-benzothienyl-substituted 6-(2-imidazolinyl)benzothiazoles-group 2, and three 2-aryl/heteroaryl-substituted 6-(2-imidazolinyl)benzothiazoles-group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential functions in cells, this study's main aim is to detect benzothiazole-based moieties with selective binding or spectroscopic response to these nucleic structures compared to regular (non-hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, selected by this method, were characterized by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and molecular modeling. Two compounds ( and ) from groups 1 and 2 demonstrated the highest affinities against 13 nucleic acid structures, while another compound () from group 2, despite lower affinities, yielded higher selectivity among studied compounds. Compound significantly inhibited RNase H. Compound could differentiate between B- (binding of dimers inside minor groove) and A-type (intercalation) helices by an induced CD signal, while both and selectively stabilized ATT triplex in regard to AT duplex. Compound induced strong condensation-like changes in CD spectra of AT-rich DNA sequences.