PhD

dissertationAntisense oligonucleotides, ribozymes, and transcription factor decoys are nucleic acid based agents. They inhibit target gene expression in a sequence-specific manner, and therefore, have great therapeutic potential. Currently, a relatively effective antisense, ribozyme, or decoy sequence is identified by testing the inhibitory activity of a series of sequences individually. Because the number of potential sequences that need to be tested is much greater than the number of sequences that can be, or is actually, tested individually, it is unlikely that the most effective sequences are identified. Due to the lack of suitable means to identify optimal or effective sequences against specific genes, it is not uncommon that a chosen sequence fails to inhibit or poorly inhibits the expression of a target gene. In this dissertation, I describe the development of a library approach for the identification of optimal antisense, ribozyme, and decoy sequences against the expression of specific genes. For this approach, libraries of antisense RNAs, ribozymes, and decoys with distinctive nucleotide sequences are derived directly from a target gene. Screening these so-called directed libraries in target cells allows the identification of the antisense, ribozyme, and decoy sequences that can ablate the expression of the target gene. I demonstrate the effectiveness of this approach by identifying the optimal antisense, ribozyme, and decoy sequences against the expression of lacZ' gene in Escherichia coli. This approach should be generally applicable for the identification of optimal antisense, ribozyme, and decoy sequences against any gene of interest