Oligo-alpha-thymidylates covalently linked to intercalating agents: circular dichroism studies of their interaction with complementary sequences.

The interaction between oligo-alpha-thymidylates covalently linked to an intercalating agent (an acridine derivative) and their complementary sequences containing beta-nucleosides (poly(rA), poly(dA), r(Ap)7rA, p(dA)8) has been studied using circular dichroism spectroscopy. Binding to poly(rA) and to poly(dA) of the modified oligonucleotides led to large changes in the induced circular dichroism signal of the acridine ring. These changes depend on whether the dye is linked to the 3'- or to the 5'-end of the oligonucleotide. Interaction with poly(rA) as well as interaction with an octadeoxyriboadenylate led to the formation of a 1A:1T complex. With poly(dA), in addition to the 1A:1T complex, a 1A:2T complex was observed when the acridine derivative was linked to the 3'-end of the octa-alpha-thymidylate. The double-stranded structures formed with poly(rA) and poly(dA) were characterized by different environments of the acridine dye. Binding to poly(rA) gave much stronger complexes than binding to poly(dA). With poly(rA) the complex was more stable when the dye was bound at the 5'-end of the oligonucleotide. Comparison between the circular dichroism changes observed upon binding at the level of polymers [poly(rA) or poly(dA)] and those obtained at the level of oligomers [r(Ap)7rA or pd(A)8] gave information relative to the position of the acridine ring in the helix.