Viscometric behavior of yeast ribosomal RNA in mixed water-organic solvent solutions and its application to a simple determination of the molecular weight

Abstract

Different samples of yeast rRNA have been studied as regards their molecular conformation in mixed water/organic solvents. In water/formamide, rRNA is in its native state at 20°C but undergoes a sharp melting transition around 43°C. On the contrary, in water/dimethylformamide and water/dimethylsulfoxide, there is already an important degree of denaturation at 20°C, which increases with organic solvent concentration. It is concluded that formamide disrupts the tertiary structure only; whereas the other solvents partially destroy the secondary structure of RNA. In water/formamide, the reduced viscosity displays a linear dependence upon concentration. In the presence of NaCl, there is only a decrease of intrinsic viscosity. With the other mixed solvents, the reduced viscosity curves present a sharp maximum, which progressively disappears when ionic strength is increased. These observations are interpreted on the basis of two effects: (i) a polyelectrolytic effect, bringing about an expansion of the semi-flexible chain in the absence of salt. (ii) An electroviscous effect producing an increase in intrinsic viscosity and a high positive dependence of reduced viscosity upon concentration. A correlation has been established between viscosity and sedimentation coefficient of various rRNA samples in 0.2 M NaCl. A relationship between sedimentation coefficient and molecular weight is also given in the same solvent. Advantage has been taken of the higher degree of extension of rRNA in some mixed water-organic solvents in order to establish a relationship between intrinsic viscosity ([η]) and molecular weight ( M r) of the form [ η] = kM a r. The empirical constants k and [α] have been determined for water 20% formamide and for 1 mM NaCl 20% dimethylsulfoxide . From the value of α, conclusions are drawn regarding the molecular conformation of rRNA in these solvents.