STUDIES OF TRINUCLEOTIDE CONFORMATIONS . ROLE OF GUANINE RESIDUES IN AN OLIGONUCLEOTIDE CHAIN

A comparison of spectroscopic (circular dichroism) and thermodynamic properties of various trinucleotides studied at different conditions of ionic strength, nucleotide concentration, and temperature, allows one to detect the conformational characteristics of polynucleotide chains, i.e., the unstacked, single-stranded stacked, and double- or multiplestranded helical associative forms. Several trinucleotides can form, at low temperatures, single-stranded stacked structures, e.g., ApApUp, ApApCp, and GpApUp. Thermodynamic analysis of the thermal “melting” process gives a relatively small value of ΔF° for the guanine-containing trinucleotide. This suggests a tendency of guanine to unstack. The presence of guanine residues probably has a dual role. In trinucleotide sequences like GpGpC or GpGpU, the formation of intermolecular associations is observed under appropriate conditions. In other sequences, e.g., ApGpU, UpGpA, and GpUpA, there is no evidence for the formation of dissymmetrical stacked base conformation under conditions favoring the formation of single-stranded structures. Our results suggest the existence of syn and anti conformers whenever unpaired guanosine residues are next to uridine. © 1969, American Chemical Society. All rights reserved.