Study on the binding of base-mismatched oligonucleotide d(GCGAGC)2 by cobalt(III) complexes

The binding of [Co(phen)(2)(HPIP)]Cl-3 and [Co(phen)(2)(DPQ)]Cl-3 to the oligonucleotide d(GCGAGC)(2) containing two sheared G:A mispairs has been studied by NMR spectroscopy for the first time. For both the complexes, a considerable number of intermolecular NOEs were observed in NOESY spectra of the cobalt-complex-bound hexanucleotide. The results suggest that [Co(phen)(2)(HPIP)]Cl-3, with HPTP, intercalates between the G(3):A(4) base pairs from the minor groove and extends to the major groove, and [Co(phen)(2)(DPQ)](3+) binds to the terminal G(5):C-6 region from two directions. P-31 NMR spectroscopy indicates that [Co(phen)(2)(HPIP)]Cl-3 binding induces a change in the phosphate backbone in the region of the mismatched base pairs, while [Co(phen)(2)(DPQ)](3+) does not cause obvious changes in the backbone. Melting experiments indicate that [Co(phen)(2)(HPIP)]Cl-3 stabilizes the double-strand structure, while [Co(phen)2(DPQ)]Cl-3 cause the duplex to untwist. (c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005.