Synthetic coenzymes for in vitro selection of DNA enzymes.

Abstract

Over the past 10 years a number of catalytically active single-stranded DNA molecules (deoxyribozymes) have been isolated from combinatorial libraries (pools) of randomized oligonucleotides. These enzyme-like DNAs customarily utilize divalent metal ions as cofactors in their catalysis. The metal ion cofactors are important because they can participate in both the correct folding of the deoxyribozymes and in the acid/base catalysis. In a new approach, we have designed and synthesized a group of potential small molecule coenzymes, designated as the IDA-oligonucleotide coenzyme, the bis-histidine aromatic coenzymes and the bis-imidazole peptide coenzymes, which could be used by deoxyribozymes in the hydrolysis of a target RNA phosphoester. It was hoped that careful design would provide these molecules with a balance of solubility, binding, and catalytic power. These synthetic coenzymes were included in combinatorial selection experiments aimed at isolating coenzyme-dependent deoxyribozymes from a randomized pool of DNA. Kinetic analysis of deoxyribozymes obtained in these experiments showed a rate enhancements that were dependent on the coenzyme used in the selection. Results of pH-dependent activity profiles of several deoxyribozymes/coenzyme systems suggest a catalytic role for the coenzyme imidazoles. In conclusion, we have demonstrated that combinatorial selection techniques can be used to select for coenzyme-dependent deoxyribozymes. This convenient methodology provides the opportunity to utilize the power of synthetic organic chemistry for the invention of novel coenzymes optimized for desired transformations. In addition, the methodology described in this dissertation complements rational design approaches, and provides a unique opportunity for the study of various aspects of enzyme/coenzyme design.