The projects inwhich I am involved with focus on the discovery of novel binding target sites for specific RNA-binding ligands to 16S ribosomal RNA of bacteria. The major approaches that I am planning to employ for this are in vitro selection methods, such as Phage Display and SELEX. Our current focus involves screening bacterial helix 21 of 16S rRNA. There is a characteristic difference between helix 21 of Escherichia coli 16S rRNA and helix 21 of Homo sapiens 18S rRNA, and that is the location of an asymmetric internal loop, a two-base (UA) bulge and a one-base (A) bulge. These internal loop and bulge sites have also been implicated as protein and small-molecule binding sites. These studies will enable us to develop small molecules as therapeutic agents targeting specific structures of RNA and may play a critical role in the development of effective RNA-binding drugs.
