Site-Specific Cleavage of RNA by a Metal-Free Artificial Nuclease Attached to Antisense Oligonucleotides

Abstract

RNA cleaving tris(2-aminobenzimidazoles) have been attached to DNA oligonucleotides via disulfide or amide bonds. The resulting conjugates are effective organocatalytic nucleases showing substrate and site selectivity as well as saturation kinetics. The benzimidazole conjugates also degrade enantiomeric RNA. This observation rules out contamination effects as an alternative explanation of RNA degradation. The pH dependency shows that the catalyst is most active in the deprotonated state. Typical half-lifes of RNA substrates are in the range of 12-17 h. Thus, conjugates of tris(2-aminobenzimidazoles) can compete with the majority of metal-dependent artificial nucleases.

miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells

“…Over the last couple of decades, some progress has been achieved in the field of designing siteselective artificial ribonucleases [42][43][44][45][46][47][48][49][50][51][52][53][54]. It was shown that short peptides, containing either alternating leucine and arginine residues or imidazole-based catalytic groups, conjugated to antisense oligonucleotides targeting tRNA, were able to hydrolyze linkages adjacent to an oligonucleotide-binding site without involvement of exogenous species such as metal ions, enzymes or cofactors (e.g., RISC, RNase H) [42,44,45,47,50,51].…”

Design of artificial nucleases and studies of their interaction with DNA

“…Reported results have shown that some small organic molecules, such as guanidine derivatives [15−17] , cyclodextrin derivatives [39,40] , macrocyclic polyamines [41] and peptides [42] , can cleave active phosphate diester and RNA. Göbel et al [43,44] put forward the concept of "metal free catalysis" and synthesized compounds 22a and 22b containing three guanidine side arms, which can catalyze RNA hydrolysis without metal ions. Furthermore, they attached 22b to DNA oligonucleotides by amide bonds to form artificial nucleases 23a and 23b containing both recognition group and catalytic hydrolytic group, which are named "metal-free nuclease" by the authors.…”

“…Furthermore, they attached 22b to DNA oligonucleotides by amide bonds to form artificial nucleases 23a and 23b containing both recognition group and catalytic hydrolytic group, which are named "metal-free nuclease" by the authors. Compounds 23a and 23b have been successfully used to hydrolyze RNA sequence selectively [44] .…”

Site-Selective Artificial Ribonucleases and their Applications

“…Conjugation of various catalysts (other lanthanide(III) complexes, multi-nuclear metal complexes, or organic molecular scissors in Fig. (2) and (3) with DNA oligomers was also effective for site-selective RNA scission [24][25][26][27][28][29][30][31][32][33][34].…”