Crystal structure of a DNA catalyst.

Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules.

Deoxyribozyme-mediated ligation for incorporating EPR spin labels and reporter groups into RNA.

Preparation of site-specifically labeled RNA for spectroscopic studies is a multistep process and requires handling of delicate samples. This chapter is focused on the synthesis of spin-labeled RNA using convertible nucleosides and the application of the deoxyribozyme 9DB1* for the ligation of RNA fragments. The convertible nucleoside approach enables the attachment of nitroxyls as paramagnetic reporters at the exocyclic amino groups of cytidine, adenosine, and guanosine nucleobases in synthetic RNA.

Enzymatic combinatorial nucleoside deletion scanning mutagenesis of functional RNA.

We describe a general and simple method to identify catalytically and structurally important nucleotides in functional RNAs. Our approach is based on statistical replacement of each nucleoside with a non-nucleosidic spacer (C3 linker, Δ), followed by separation of active library variants and readout of interference effects by analysis of enzymatic primer extension reactions.