Thermodynamic studies on selective recognition of bases in complex formation between base pairs. Formation of complexes by non-complementary interactions

Abstract

In order to obtain information on non-complementary interaction in polynucleotide mixtures, the molecular conformations of the equimolar mixtures poly(A)—poly(C) (Mixture 1), poly(A)—poly(I) (Mixture 2), poly(C)—poly(U) (Mixture 3), and poly(I)—poly(U) (Mixture 4), in concentrated solutions, were studied by means of microcalorimetry, spectrophotometry, refractive index, and ab initio molecular orbital (MO) calculation. Mixtures 1 and 3 did not form complexes by non-complementary interaction under the experimental conditions of the present work, although possible interactions were considered for both systems from the standpoint of the net charge, using ab initio molecular orbital (MO) calculations. The phase state for the poly(I)—poly(C) mixture based on complementary interaction between purine and pyrimidine bases was observed using a polarization microscope. This indicated that the poly(I)—poly(C) mixture forms a layered liquid crystal, as reported previously for poly(A)—poly(U) mixture. It should be noted that Mixture 2 forms liquid crystals with a triple-stranded helical structure by non-complementary interaction between poly(A) and poly(I), both with purine base. Moreover, the change in enthalpy Δ H t (7.3 kJ) based on the helix—coil transition of Mixture 2 is approximately the same as those of poly(I)—poly(C) mixture (Δ H t = 6.2 kJ) and poly(A)—poly(U) mixture (Δ H t = 6.4 kJ), as reported previously. But the change in enthalpy (Δ H ord—disord = 2.7 kJ) based on the order—disorder transition of the layered liquid crystal for Mixture 2 is different from the value Δ H ord—disord = 5.8 kJ for an equimolar poly(I)—poly(C) mixture, and Δ H ord—disord = 6.6 kJ are for equimolar poly(A)—poly(U) mixture, in which liquid crystals are formed by complementary interaction, suggesting that the intermolecular interaction of the liquid crystals formed by non-complementary interaction between the purine bases of poly(A) and poly(I) is very weak compared with that formed by complementary interaction between purine base and pyrimidine base of nucleotides. Mixture 4 displays an isotropic phase at concentration below 5.0 wt%, and an anisotropic phase with a double-stranded helical structure appears above 5.0 wt%. But the changes in enthalpy (Δ H t = 4.0 kJ) and Δ H ord—disord = 1.0 kJ), for Mixture 4 are smaller than those for Mixture 3, poly(I)—poly(C), and poly(A)—poly(U) by complementary interaction, as reported previously, demonstrating that the molecular conformation formed between purine and pyrimidine bases of Mixture 4 is different from that formed between purines or between purine and pyrimidine bases.