CD of the synthetic RNA duplexes poly[r(A-T)] and poly[r(A-U)] in salt and ethanolic solutions.

Synthetic RNA polyr(A-T)] has been synthesized and its CD spectral properties compared to those of polyr(A-U)], polyd(A-T)], and polyd(A-U)] in various salt and ethanolic solutions. The CD spectra of polyr(A-T)] in an aqueous buffer and of polyd(A-T)] in 70.8% v/v ethanol are very similar, suggesting that they both adopt the same A conformation. On the other hand, the CD spectra of polyr(A-T)] and of polyr(A-U)] differ in aqueous, and even more so in ethanolic, solutions. We have recently observed a two-state salt-induced isomerization of polyr(A-U)] into chiral condensates, perhaps of Z-RNA M. Vorlícková, J. Kypr, and T. M. Jovin, (1988) Biopolymers 27, 351-354]. It is shown here that polyr(A-T)] does not undergo this isomerization. Both the changes in secondary structure and tendency to aggregation are different for polyr(A-T)] and polyr(A-U)] in aqueous salt solutions. In most cases, the CD spectrum of polyr(A-U)] shows little modification of its CD spectrum unless the polymer denatures or aggregates, whereas polyr(A-T)] displays noncooperative alterations in its CD spectrum and a reduced tendency to aggregation. At high NaCl concentrations, polyr(A-T)] and polyr(A-U)] condense into psi(-) and psi(+) structures, respectively, indicating that the type of aggregation is dictated by the polynucleotide chemical structure and the corresponding differences in conformational properties.