Pulsed electric linear dichroism of double-stranded antiparallel poly(rA)center dot poly(rU) and poly(dA)center dot poly(dT) helices in solution

Reduced electric linear dichroism (ELD), Delta epsilon/epsilon, Of the title duplexes in ionic solutions was measured at 7 degrees C in the 1.5-24 kV/cm field strength and 300-190 nm wavelength regions. The rodlike (rA)(n) .(rU)(n) and (dA)(n) .(dT)(n) samples, whose counterion was Mg2+ in most cases, were prepared by sonication and subsequent fractionation. The weight-average molecular weight and molecular weight distribution of each fraction, determined by the GPC/LALLS method, were taken into account in the analysis of the field strength dependence of Delta epsilon/epsilon values. These values were fitted to theoretical orientation functions to evaluate the saturated reduced dichroism, (Delta epsilon/epsilon)(s), at absorption peaks. The wavelength dependence of (Delta epsilon/epsilon),, the ELD spectrum, was undulatory in the 300-190 nm region. The isotropic absorption and second-derivative spectra of each duplex were decomposed into eight component bands, which were assigned to constituent bases. The analysis of ELD spectrum revealed that the individual bases are both tilted and rolled in the rA rU and dA dT base pair and that the planes are bent. From transient dichroism signals, the weight-average rotational relaxation time, tau(w), was obtained, from which the axial translation per base pair, h, was evaluated. The limiting h values were found to be ca. 2.6 Angstrom for (rA)(n) .(rU)(n) and ca. 3.0 Angstrom for (dA)(n) .(dT)(n). Thus, both duplexes were concluded to belong to the A-form family.