Toward an RNaseA Mimic:  A DNAzyme with Imidazoles and Cationic Amines

Abstract

Site-specific RNA cleavage has received considerable attention over the years. Directed synthesis to append imidazoles or amines or both to oligonucleotides to target specific RNA cleavage represents an exciting avenue of research. However, to date catalysis by such synthetic constructs, particularly in terms of turnover, has been difficult to observe. This is the first report of a truly catalytic M2+-independent DNAzyme synthetically modified with imidazoles and cationic amines that would seem to mimic RNaseA. This work now demonstrates how synthetic organic chemistry, when merged with combinatorial selection, can result in a new class of DNAzymes that meets the ongoing synthetic challenges for developing relatively small biomimetic catalysts.

A Highly Selective DNAzyme Sensor for Mercuric Ions

“…[40] Both functionalized nucleosides were incorporated enzymatically from triphosphate (TP) precursors [41] (Figure 1 a) in an in vitro selection that led to the discovery of 9 25 -11. The self-cleaving 9 25 -11c was subsequently converted to 9 25 -11t, the transcleaving species, [42] which exhibited multiple turnover. [43] The introduction of two amino acid side chains reminiscent of the active site of RNaseA confers both electrostatic complementarity and acid/base catalysis to this DNAzyme.…”

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating a Cationic Functionality

“…In vitro selection is a combinatorial technique that generates receptors, ligands, and catalysts from nucleic acid libraries containing as many as 10 14 -10 16 different molecules and is a powerful method to explore the sequence space of biopolymers in search of functional domains. Some effort has been devoted to developing in vitro selection processes that use modified monomer triphosphates as substrates for polymerases (27)(28)(29)(30)(31)(32)(33)(34)(35)(36), and several in vitro selection experiments have been undertaken to select for catalysts or aptamers whose functions depend on the presence of modified nucleotides (37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48), with notable success (39,40,(43)(44)(45)(46)(47). On the other hand, modified building blocks have not proven to always be critical in obtaining superior receptors or catalysts (40,42,48,49).…”

Synthesis of Functionalised Nucleosides for Incorporation into Nucleic Acid-Based Serine Protease Mimics

“…Since incorporation of unprotected imidazole building blocks into oligonucleotides has been accomplished in some cases, we also directly coupled urocanic acid (1) to dimethoxytrityl protected 2'-amino-2'-deoxyuridine 4 [40,41]. This was achieved using EDC and NHS, yielding the desired compound 6 in only moderate yield [42,43].…”