Site-Selective Artificial Ribonucleases and their Applications

Abstract

Recent developments in artificial enzymes for site-selective scission of RNA have been reviewed, and their advantages over ribozymes are discussed. Most of previous reports involve covalent fixation of molecular scissors to sequence-recognizing moieties. However, non-covalent strategy, in which these two components are never covalently bound each other, has made remarkable progresses. When oligonucleotide bearing an acridine (site-selective activator) forms duplex with RNA substrate, the phosphodiester linkage of the RNA in front of the acridine is selectively activated and hydrolyzed by various metal ions (e.g., Lu(III). These non-covalent artificial ribonucleases are simple enough to be used for various more complicated systems. For example, tandem activator for clipping of desired fragment from long RNA substrate is obtained by attaching two acridines to an oligonucleotide. By analyzing the resultant RNA fragment with MALDI-TOFMS, the RNA substrate is accurately genotyped in terms of both single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (Indels).

Mercury(II)-Catalyzed Cleavage, Isomerization and Depurination of RNA and DNA Model Compounds and Desulfurization of Their Phosphoromonothioate Analogs

“…Metal ion-catalyzed cleavage of both RNA and DNA phosphodiester linkages has been investigated extensively to understand the mechanism of action of natural nucleases (including ribozymes) [1][2][3][4][5], as well as to develop artificial ones [6][7][8][9][10]. Comparative studies with phosphodiester and phosphorothioate model compounds have been instrumental in revealing coordination of catalytically important metal ions to the scissile linkage [11][12][13][14][15][16].…”

A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M 2+ )

“…The significance of M 2+ -independent RNases is further underscored in numerous reports on oligonucleotides synthetically endowed with various cationic amines, guanidines and imidazoles–functionalities that are found at the active sites of e.g. RNase A ( 48 , 49 ).…”

2'-O-Methyloligoribonucleotide based artificial nucleases (2’-O-MeOBAN’s) cleaving a model of the leukemia related M-BCR/ABL m-RNA

“…1 and several studies demonstrate the potential for targeting biologically relevant RNAs with artificial ribonucleases. [2][3][4] All systems developed so far clearly still have some distance to go in order to achieve rates efficient enough for use in a therapeutic setting. However, in order for efficient systems to evolve for a particular target it seems logical that development of artifical nuclease systems should be moved to a setting that incorporates a sequence that is identical to that of a particular target.…”