This work will focus on the analysis of populations of large RNA molecules (200-250 nucleotides) that have been selected to bind to human immunodeficiency virus reverse transcriptase protein with unusually strong affinities (sub-picomolar) in vitro, or to catalyze chloramphenicol acetyl transfer (CAT activity) in vivo. Binding at this level of affinity and in vivo catalysis both represent notable challenges for RNA, and it will be of interest to determine the exact structural features of each that give rise to their respective functions. The HIV work, in particular, will shed light on interactions between RNA and HIV reverse transcriptase, and it may lead to novel approaches to anti-AlDS therapies. Individual isolates from each population will be cloned and sequenced, and their respective biochemical behaviors (binding and inhibition constants, catalytic properties) will be correlated with their individual nucleotide sequences. Upon determination of the minimal sequence elements required for activity, the minimal elements will be synthesized and characterized in great detail as to binding and inhibition constants, catalytic properties, and secondary structure. Finally, site-directed mutagenesis will be used to asses the roles of individual nucleotides.
Burke, D H; Hoffman, D C (1998) A novel acidophilic RNA motif that recognizes coenzyme A. Biochemistry 37:4653-63 |
Burke, D H; Hoffman, D C; Brown, A et al. (1997) RNA aptamers to the peptidyl transferase inhibitor chloramphenicol. Chem Biol 4:833-43 |
Burke, D H; Scates, L; Andrews, K et al. (1996) Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. J Mol Biol 264:650-66 |