RNA structural dynamics: pre-melting and melting transitions in E. coli 5S rRNA

The temperature dependent transition from duplex to a single strand in E. coli 5S ribosomal RNA is a multistep process, and it involves intermediate states. We have analyzed these structural dynamics by chemical modification of cytidines and by single strand specific nuclease digestions. This combined approach led to the characterization of premelting and melting transitions within individual structural segments of the native macromolecule, which we feel may find general application to the structure of biological polyribonucleotides: 1) G-C base pairs at the termini of helices are relatively unstable and they readily undergo premelting transition. 2) Internal G-U/A-U rich stretches of helices exhibit dynamic premelting properties. 3) Hairpin loops have a relatively stronger destabilizing effect than internal loops. 4) Bulge loops destabilize the neighbouring base pairs. 5) Melting of helical segments occurs starting from the destabilizing structures listed above, preferentially from the helix termini. E. coli 5S rRNA has been shown to adopt different conformations. The presence of urea leads to induction of enhancement in the sensitivity for nuclease S1 at several nucleotide positions. The possibility of structural rearrangements will be discussed.

Dynamics of ribosomal RNA structure

The structural dynamics of ribosomal 5S RNAs have been investigated by probing single strandedness through enzymatic cleavage and chemical modification. This comparative study includes 5S rRNAs from E. coli, B. stearothermophilus, T. thermophilus, H. cutirubrum, spinach chloroplast, spinach cytomplasm, and Artemia salina. The structural studies support a unique tertiary interaction in eubacterial 5S rRNAs, involving nucleotides around positions 43 and 75. In addition long range structural effects are demonstrated in E. coli 5S rRNA due to the conversion of C to U at position 92.

Physical studies on a nucleoprotein from the ribosome of E. coli

Bacterial 5S RNA and its cognate proteins constitute an attractive system to study nucleoprotein interactions. The molecular weights of the components involved are modest and they can be prepared in the quantities necessary to permit the application of material-intensive techniques like NMR and X-ray crystallography. 5S RNA is being examined by proton NMR at 500 MHz with special attention paid to the downfield NH proton region. A substantial number of assignments can be suggested in this region based on nuclear Overhauser results. The binding of protein L25 (E. coli) to the RNA gives rise to a highly characteristic set of perturbations in the spectrum of the RNA. The data suggest a localized and assignable alteration in RNA structure upon formation of the complex. In addition we have grown large crystals of RNAs related to 5S RNA and their complexes with a cognate protein. The properties of these crystals and the progress made in analyzing their structure are discussed.