Ribozymes and RNA Structure
The research program in my laboratory focuses on catalytic RNA molecules, or ribozymes. We are working with two fundamentally different ribozymes that catalyze RNA processing reactions, the hairpin ribozyme derived from the satellite RNA of tobacco ringspot virus, and group I introns from bacterial, nuclear, and mitochondrial genomes. Since catalytic RNA has been known to exist for only a short time, relatively little is known about the structure and action of these molecules. Research projects include those that address fundamental problems of RNA structure and catalytic mechanism, and also projects aimed towards developing engineered ribozymes to serve as antiviral agents in the laboratory and, potentially, in clinical settings. We employ a wide range of methods, including those of molecular biology, genetics, enzymology and cell biology. Currently, we are focusing on the structure and catalytic mechanism of three molecules, the hammerhead, hairprin and glmS ribozymes.
Model of the active structure of the hammerhead ribozyme
Burke Research Group
Gaur, S., Heckman, J. E. and Burke, J. M. Mutational inhibition of ligation in the hairpin ribozyme: substitutions of conserved nucleobases A9 and A10 destabilize tertiary structure and selectively promote cleavage. RNA 2008 Jan;14(1):55-65
Lambert, D., Heckman, J.E. and Burke J.M.. Three conserved guanosines approach the reaction site in native and minimal hammerhead ribozymes. Biochemistry. 2006 Jun 13;45(23):7140-7.
Lambert, D., Heckman, J.E. and Burke, J.M. Cation-specific structural accommodation within a catalytic RNA. Biochemistry. 2006 Jan 24;45(3):829-38.
Han, J. and Burke, J.M. Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site. Biochemistry. 2005 May 31;44(21):7864-70.
Heckman, J.E., Lambert, D. and Burke, J.M. Photocrosslinking detects a compact, active structure of the hammerhead ribozyme. Biochemistry. 2005 Mar 22;44(11):4148-4156.
Zhang, Z. and Burke, J.M. Inhibition of viral replication by ribozyme: mutational analysis of the site and mechanism of antiviral activity. J Virol. 2005 Mar;79(6):3728-3736.
Pinard, R., Hampel, K.J., Heckman, J.E., Lambert, D., Chan, P.A., Major, F., Burke, J.M. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J. 2001 Nov 15;20(22):6434-6442.