Bio-Physical Studies of Modified Ribosomal RNAs

Our group is interested in the intersubunit bridge region of the ribosome, which involves interactions between the 16S and 23S rRNAs. The 16S rRNA makes contacts with 23S rRNA through the A site, which is also an important site for tRNA binding and a known target site for aminoglycoside antibiotics. The 23S rRNA contacts 16S rRNA through helix 69 (H69), which also interacts with the Aand the P-site tRNAs. H69 is a dynamic region of the ribosome and contains conserved pseudouridine residues at positions 1911, 1915, and 1917. In order to better understand the role of the modified nucleosides, pseudouridine and its analogues, 3-methylpseudouridine and 3methyluridine, were synthesized and incorporated into RNA at specific locations. The stabilities and structures of the RNAs were examined by using thermal melting, circular dichroism, and NMR spectroscopy. We are also working on the pH effects on the structure of loop region and contribution of pseudouridine towards the pH-dependent stability.