[Compact structure of the small E. coli ribosomal subunit and its RNA studied by fluorescence spectroscopy and...

Analysis of the temperature dependence of fluorescence polarization of ethidium bromide adsorbed on the double helical fragments of 16S RNA's hairpin loops was used to characterize the intramolecular flexibility of RNA in the free state and within 30S subunit. We show that the local mobility of RNA segments is strongly limited by the tertiary structure of 16S RNA and ribosomal proteins reinforce these limitations. It was suggested that the mechanism of the temperature dependent RI particle activation involved the temporary increase of the local mobility of RNA segments in RNP which favored the formation of the new intraribosomal contacts. A comparison of sw 20 dependences of RNA and 30S subunit on Mg+ and K+ concentrations leads to the proposal that RNA in the small subunit in the physiological conditions has the stressed conformation. This conformation is maintained by the Mg2+-dependent RNA-RNA interactions induced by ribosomal proteins and specific only for the subunit.