Deoxyribonucleoside triphosphates (dNTPs) are activated building blocks that are fundamental in the polymerase-mediated natural biosynthesis of DNA. Chemical modification of triphosphates at various locations followed by polymerization is a convenient and versatile way for the introduction of functional groups into nucleic acids. In addition, if the modified dNTPs are substrates for polymerases in both primer extension reactions (PEX) and polymerase chain reactions (PCR), then they can serve in SELEX (Systematic Enrichment of Ligands by Exponential Enrichment) for the generation of oligonucleotides binding to specific targets (aptamers) or catalytic DNAs (DNAzymes). In SELEX and related methods of combinatorial methods of in vitro selection, a large population of oligonucleotides (10^12 sequences) is examined in parallel for binding affinity or catalytic properties.
The projected work is heavily based on the original grant (PZ00P2_126430) and involves the use of modified dNTPs in in vitro selection experiments for the discovery of catalytic nucleic acids. Indeed, I have synthesized a variety of dNTPs bearing residues that are of primordial importance in organocatalysis. In addition, all these dNTPs were shown to be good substrates for both PEX and PCR and can thus be used in SELEX for the generation of DNAzymes catalyzing organic reactions in water. Moreover, dNTPs bearing carboxylic acid, imidazole, and guanidine residues are currently being synthesized and could be used in the selection of DNAzymes capable of catalyzing the scission of amide bond linkages.
In summary, the ultimate goal of this SNF grant is the discovery of DNAzymes with hitherto unknown properties, which in turn could provide significant improvements in the field of catalytic nucleic acids and could have deep ramifications in fundamental research and therapeutical applications. For instance, DNAzymes acting as artificial proteases could be used in the development of new drugs especially towards amyloid diseases such as Alzheimer's, while DNAzymes catalyzing organocatalytic reactions in water could be converted into valuable synthetic tools.