A COMPARATIVE-STUDY ON THE STRUCTURE OF DOUBLE-STRANDED ANTIPARALLEL POLY(RIBOGUANYLIC ACID)CENTER-DOT-POLY(RIBOCYTIDYLIC ACID) AND POLY(DEOXYRIBOGUANYLIC ACID)CENTER-DOT-POLY(DEOXYRIBOCYTIDYLIC ACID) HELICES IN SOLUTION BY PULSED ELECTRIC LINEAR DICHROISM

The sonicated and fractionated poly(rG). poly(rC) (I) and poly(dG). po ly(dC) (II) samples mostly with Na+ counterions were studied, on a com parative basis, to determine the spatial arrangement of the constituen t G and C bases with respect to the double-stranded helical axis in io nic aqueous solutions. The reduced electric linear dichroism, Delta ep silon/epsilon, was measured at 7 degrees C in 1.5-24 kV/cm field stren gth and 300-190 nm wavelength regions. By analyzing the field strength dependence of observed Delta epsilon/epsilon values with theoretical orientation functions, the saturated reduced dichroism, (Delta epsilon /epsilon)(s), at 260 nm was evaluated to be -0.96 +/- 0.02 for I and - 0.93 +/- 0.01 for II. The electric linear dichroism (ELD) spectra of t hese duplexes are very close to each other, being undulatory, but not constant, in the whole wavelength region. The (Delta epsilon/epsilon)( s) values are never as high as -1.5, indicating that the optical trans ition moments of the nucleic acid bases responsible for the UV absorpt ion bands are not normal to the helix axis. By analyzing the ELD spect ra with a newly developed technique, the inclination angle alpha, the roll angle theta(R), and the tilt angle theta(T) were evaluated for th e individual bases. The most likely values are 24 degrees, 1 degrees, and 24 degrees for rG; 26 degrees, 1 degrees, and 26 degrees for rC in the rG . rC base pair; 26 degrees, 2 degrees, and 26 degrees for dG; 29 degrees, 3 degrees, and 29 degrees for dC in the dG . dC pair. Thus , the base pairs are only slightly bent and propeller twisted, being n early coplanar. Both duplexes were concluded to exist in the same conf ormation and to belong to the same A-form family in solutions in spite of the different sugar structure, contrary to X-ray results in the so lid state.