Journal of Physical Chemistry B, Vol.101, No.5, 837-845, 1997
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). poly(dC) (II) samples mostly with Na+ counterions were studied, on a comparative basis, to determine the spatial arrangement of the constituent G and C bases with respect to the double-stranded helical axis in ionic aqueous solutions. The reduced electric linear dichroism, Delta epsilon/epsilon, was measured at 7 degrees C in 1.5-24 kV/cm field strength 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 these 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 transition moments of the nucleic acid bases responsible for the UV absorption bands are not normal to the helix axis. By analyzing the ELD spectra with a newly developed technique, the inclination angle alpha, the roll angle theta(R), and the tilt angle theta(T) were evaluated for the 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 nearly coplanar. Both duplexes were concluded to exist in the same conformation 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 solid state.
Keywords:MOLECULAR-WEIGHT DISTRIBUTION;DEOXYRIBONUCLEIC-ACID;AQUEOUS-SOLUTIONS;NUCLEIC-ACIDS;ULTRASONIC SCISSION;TRANSITION MOMENTS;FIELD;BIREFRINGENCE;SPECTRA;DNA