Tertiary structure of tRNAPhe (yeast): kinetics and electrostatic repulsion

Conditions were established that allowed the observation of the unfolding of the tertiary structure of tRNAPhe (yeast) without the interference of either secondary structure or low salt aberrant structures. Relaxation kinetics of tertiary structure melting show that the reaction proceeds according to co-operative all-or-none mechanism. The negative activation enthalpy of formation (delta H+ + R = -14 +/- 5 kcal/mol, -59 +/- 21 kJ/mol) implies a fast pre-equilibrium preceding the rate-limiting step. The ionic strength dependence of the corresponding rate constant demonstrates that most of the electrostatic repulsion characteristic of tertiary structure folding is overcome before the rate-limiting step is reached. On the other hand, most of the stabilizing enthalpy change occurs after the rate-limiting step. At the usual ionic strength (0.1 M Na+) tertiary structure folding is about 100 times slower than double-helix formation. Extrapolation of the rate constants to high ionic strengths, however, indicates that the dynamic differences between secondary and tertiary structure are only due to electrostatic repulsion. The stabilization of tertiary structure by alkaline salts is increased by decreasing the cationic radius. Double helices show virtually no dependence on the radius of monovalent cations. This indicates considerable geometric restrictions for the stabilization of tertiary structure.