Ionic strength dependent conformational changes of transfer ribonucleic acid studied by circular polarization of...

The circularly polarized phosphorescence emitted by the 4-thiouridine base was measured for bulk Escherichia coli tRNA, E. coli tRNA1Val, E. coli tRNAfMet, and E. coli tRNAPhe as a function of ionic strength in the presence of 1 mM Mg2+. The emission anisotropy factor, gem, was found to be dependent on the degree of local stacking in the vicinity of the chromophore. For bulk tRNA and tRNAfMet a marked similarity was observed between the behavior of gem and the translational diffusion coefficient D020,w [Pots, R. O., Wang, C. C., Fritzinger, D. C., Ford, N. C. & Fournier, M. J. (1979) in Cold Spring Harbor Monograph Series (Schimmel, P. R; Söll, D., & Abelson, J. N., Eds.) Part A, p 207, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY]. This was interpreted to mean that a relationship exists between the local stacking around the 4-thiouridine chromophore and the overall general similarity of behavior was observed, each species of tRNA examined exhibited a distinctive dependence of conformation on salt concentration. tRNAPhe was found to be a particular exception in the low-salt region (less than 50 mM). The value of the phosphorescence anisotropy factor was found to be remarkably larger (about 50-fold). Thus minor conformational changes in the tRNA molecule are more readily detected by circular polarization of phosphorescence than by circular dichroism