The ligand-structure-selective binding of oligonucleotide by cobalt complexes

The binding of two Co(III) complexes [Co(phen)2(DPQ)]3+ and [Co(phen)2(HPIP)]Cl3 [HPIP = 2-(2-hydroxyphenyl) imidazo [4,5-f][1,10] phenanthroline, DPQ = dipyrido[3,2-f:2′,3′-h]quinoxaline] to the normal base-paired decanucleotide d(CCTAATTAGG)2 was studied by 2D NMR. The results indicate that the width of intercalating ligand has a large effect on the selectivity of binding site. For [Co(phen)2(HPIP)]Cl3, the complex binds the decanucleotide at C2T3:G9A8 and A4A5:T7T6 by intercalation from the minor groove, while [Co(phen)2(DPQ)]3+ intercalates into T3A4:T7A8 region from the minor groove. The conclusion was further proved by molecular modeling.