bioorganic chemistry; DNA enzymes; Enzyme mimics; Modified Nucleobases
Hollenstein Marcel (2012), Nucleoside Triphosphates — Building Blocks for the Modification of Nucleic Acids, in Molecules
, 17, 13569-13591.
Hollenstein Marcel, Wojciechowski Filip, Leumann Christian (2012), Polymerase incorporation of pyrene-nucleoside triphosphates, in Bioorg. Med. Chem. Lett.
, 22, 4428-4430.
Hipolito CJ, Hollenstein M, Lam CH, Perrin DM (2011), Protein-inspired modified DNAzymes: dramatic effects of shortening side-chain length of 8-imidazolyl modified deoxyadenosines in selecting RNaseA mimicking DNAzymes, in ORGANIC & BIOMOLECULAR CHEMISTRY
, 9(7), 2266-2273.
Hollenstein Marcel (2011), Expanding the Catalytic Repertoire of DNAzymes by Modified Nucleosides, in Chimia
, 65, 770-775.
Lam Curtis H., Hipolito Christopher J., Hollenstein Marcel, Perrin David M. (2011), A divalent metal-dependent self-cleaving DNAzyme with a tyrosine side chain, in Org. Biomol. Chem.
, 9, 6949-6954.
Hollenstein Marcel, Synthesis of deoxynucleoside triphosphates that include proline, urea, or sulfonamide groups and their polymerase incorporation into DNA, in Chem. Eur. J.
DNAzymes are DNA molecules able to catalyze a variety of reactions and unlike their RNA counterpart, have no precedent in nature. Consequently, DNAzymes are obtained artificially by molecular evolution-based combinatorial techniques such as SELEX (systematic evolution of ligands by exponential enrichment). The prevalent application to which many in vitro selection experiments still strive, is the use of DNAzymes as catalytic antisense agents for the specific cleavage of mRNA leading to gene silencing. Even though the knowledge gathered on deoxyribozymes advances at a quick pace and numerous applications are emerging, important gaps still need to be filled. Indeed, the use of DNAzymes adorned with chemical functionalities could drastically increase the number and nature of the catalyzed chemical reactions. Moreover, due to the ease of selection for catalytic activity and synthetic scale-up, DNAzymes represent a potential interesting class of catalyst that may find application in organic synthesis, provided their solubility in organic media is increased. Finally, in vitro selections are often lengthy procedures that lead to self-cleaving deoxyribozymes that need to be re-engineered to trans-cleaving species to achieve multiple turnover catalysis. Consequently, new methods that could reduce the length of the procedure and yield directly trans-acting deoxyribozymes could be of high benefit.The general aim of the project presented herein, is to increase the potency and usefulness of DNAzymes as catalysts by increasing their catalytic and chemical repertoire, their solubility in organic media and their resistance to nuclease degradation. To this end, the project is divided in three sections, each of which dealing with one of these facets of the mentioned projected improvements:1) In vitro selection of an LNAzyme acting as an RNase mimic. The aim of this part of the project is to use known locked nucleic acid (LNA) triphosphate units for an in vitro selection experiment to discover a DNAzyme with enhanced catalytic properties and stability to nuclease degradation. 2) Selection of a DNAzyme with peptidase-like activity. This section questions whether it is possible to find a DNAzyme catalyzing the hydrolysis of an amide bond. To this effect, a PNA/DNA chimeric substrate will be used in an in vitro selection experiment. In addition, a modified dNTP bearing a hydrophobic residue is hypothesized to facilitate the in vitro selection discovery of a DNAzyme able to function in organic medium.3) Selection using transient functional groups. A disulfide-bearing dNTP analogue will be used as anchor for the temporary attachment of various functional groups that could mediate the cleavage of a ribonucleotide linkage. This strategy used in the context of in vitro selections, could allow for the rapid discovery of DNAzymes catalyzing a broad variety of reactions.