INTERACTIONS CONTRIBUTING TO STABILITY OF A POLYNUCLEOTIDE HELICAL CHAIN ROLE OF 2'-HYDROXYL AND OF PHOSPHATE GROUPS

The role of the 2′-hydroxyl and of the phosphate groups in the formation of the dissymmetric helical conformation of polyribonucleotides was investigated by ultraviolet absorption, by circular dichroism and by infrared linear dichroism. The circular dichroism spectra and their temperature dependence were studied for various 3′ → 5′ dinucleoside phosphates containing either ribose, deoxyribose or arabinose. As low as -20° there was essentially no evidence for dissymmetric base stacking in cytidylate dimers when the sugars were arabinose or deoxyribose instead of compounds containing ribose. Comparison of isomers in which either the 3′- or 5′-linked pentose is arabinose, e.g. 3′ → 5′ arabinose-ribosyl or riboside-arabinosyl showed that the presence of arabinose in the 3′-residue caused unstacking. The corresponding 5′-arabinose isomers were found to form the ordered, dissymmetric conformation. Similar results were obtained by comparing dinucleoside phosphate isomers containing deoxyribose and ribose in 3′- or 5′-residues. These results indicated that the oligonucleotide conformational stability depended on the presence and on the configuration of the 2′-hydroxyl in the 3′-linked pentose. The role of the phosphate residue in the conformational stability was first investigated by circular dichroism in the temperature dependence of dinucleotide isomers. The thermodynamic parameters ΔH° and ΔF° at 0° for the thermal denaturation process were lower for dinucleotides with the terminal phosphate in the 3′-position as compared to the corresponding 5′-isomer or the dinucleoside phosphate. Thus, the presence of a terminal phosphate in the 3′-position favored unstacking. The infrared linear dichroism investigation in the region of the phosphate bands (1230 and 1085 cm-1) indicated the following differences between double-stranded polyribonucleotides poly A·poly U (and also poly I·poly C) and DNA: 1. 1. Deuteration of poly A·poly U causes a shift of the 1085 cm-1 band to a lower frequency with good resolution of this band into a doublet but with no changes in the corresponding DNA bands. 2. 2. In poly A·poly U the orientation of the O. . .P. . .O bisector is calculated to form an angle of about 39°, whereas in DNA it is about 70° to the helical axis. The possibility of direct or indirect interaction between the phosphate and the 2′-hydroxyl ribose groups is discussed in order to interpret these results. © 1969.