Nuclear magnetic resonance studies of complex formation between the oligonucleotide d(TATC) covalently linked to an acridine derivative and its complementary sequence d(GATA)

Abstract

The oligodeoxynucleotide d(TATC) was covalently attached to the 9-amino group of 2-methoxy-6-chloro-9-aminoacridine (Acr) through its 3''-phosphate via a pentamethylene linker (m5). Complex formation between d(TATC)m5Acr and the complementary strand d(GATA) in aqueous solution was investigated by nuclear magnetic resonance. The COSY and NOESY connectivities allowed us to assign all the proton resonances of the bases, the sugars (except the overlapping 5''/5" resonances), the acridine, and the pentamethylene chain. Structural informations derived from relative intensities of COSY and NOESY maps revealed that the duplex d(TATC).sbd.d(GATA) adopts a B-type conformation and that the deoxyriboses preferentially adopt a 2''-endo conformation. The NOE connectivities observed between the protons of the bases or of the sugars and the protons of the dye and of the pentamethylene chain led us to propose a model involving an equilibrium between two families of configurations. In the first family, the acridine derivative is intercalated between base pairs C4-G4 and T3-A3. In the second family, the acridine derivative is sandwiched between two aggregated duplexes. The structure of the intercalated complex as well as that of the aggregated species is discussed.