On the conformation of transfer RNA in solution: Dependence of denaturation temperature and structural parameters of mixed and formylmethionyl Escherichia coli transfer RNA on sodium ion concentration

There is at present considerable evidence that transfer RNA in the presence of Mg²⁺ exists in a more highly ordered state than predicted by simple cloverleaf models (Levitt, 1969; Cramer, 1970, Abstr. 8th Internat. Cong. Biochem. p. 214; Cramer, 1971). This highly ordered structure is shown here to correspond closely to that found in the presence of high concentrations of Na⁺ (2 m) at pH 6.5. As the Na⁺ counterion concentration is decreased, progressive denaturation occurs to a state finally approximating a coil. We have determined the dependence of the mid-point of the thermal denaturation profiles (T_m), ultraviolet absorbance, viscosity, circular dichroism spectra, and tritium exchange-out rates and number on counterion concentration for both unfractionated (mixed) Escherichia coli tRNA as well as the purified E. coli formylmethionine specific tRNA. The transition and physical data are consistent with a simple interpretation of the states of tRNA present as a function of ionic strength. Specifically, at pH 6.5 in the region of 0.1 to 2 m-NaCl, below 25 °C, tRNA exists as a cloverleaf with varying degrees of superstructure converging to the Mg²⁺ state. Below 0.1 m-Na⁺ denaturation of the cloverleaf structure itself takes place, representing the electrostatically induced transition to some type of coil configuration. In the vicinity of 0.1 m-Na⁺ we suggest that the average structure in solution approximates a cloverleaf conformation, although we have no information on the distribution of molecules among closely related states. This picture provides a useful reference for physical and functional studies, which may define more completely the tertiary conformation and specific biological interactions of this molecule.