Probing dynamic changes in rRNA conformation in the 30S subunit of the Escherichia coli ribosome.

Ribosomal RNA molecules within each ribosomal subunit are folded in a specific three-dimensional form. The accessibility of specific sequences of rRNA of the small ribosomal subunit of Escherichia coli was analyzed using complementary oligodeoxyribonucleotides, 6-15 nucleotides long. The degree of hybridization of these oligomers to their RNA complements within the 30S subunit was assessed using nitrocellulose membrane filter binding assays. Specifically, the binding of short DNA oligomers (hexameric and longer) complementary to nucleotides 919-928, 1384-1417, 1490-1505, and 1530-1542 of 16S rRNA was monitored, and in particular how such binding was affected by the change in the activation state of the subunit. We found that nucleotides 1397-1404 comprise an unusually accessible sequence in both active and inactive subunits. Nucleotides 919-924 are partially available for hybridization in active subunits and somewhat more so in inactive subunits. Nucleotides 1534-1542 are freely accessible in active, but only partially accessible in inactive subunits, while nucleotides 1490-1505 and 1530-1533 are inaccessible in both, under the conditions tested. These results are in general agreement with results obtained using other methods and suggest a significant conformational change upon subunit activation.