Nucleic acids, catalytic

In vitro selection strategies can be sub-divided into two types direct and indirect selections. These two types of selection experiments directed at the isolation of synthetic catalytic nucleic acids differ mainly by their technical concept, their design and their outcome. 

While indirect selections work quite well for antibodies they have been less successful in the case of catalytic nucleic acids. There are only three examples which prove that it is possible in principle to obtain a ribo- or deoxyribozyme by selecting an aptamer that binds to a TSA A rotamase ribozyme [7], a ribozyme capable of catalyzing the metallation of a porphyrin derivative [92], and one catalytic DNA of the same function [93]. Another study reported the selection of a population of RNA-aptamers which bind to a TSA for a Diels-Alder reaction but the subsequent screen for catalytic activity was negative for all individual RNAs tested [94]. The attempt to isolate a transesterase ribozyme using the indirect approach also failed [95]. 

Many examples of catalytic nucleic acids obtained by in vitro selection demonstrate that reactions catalyzed by ribozymes are not restricted to phosphodiester chemistry. Some of these ribozymes have activities that are highly relevant for theories of the origin of life. Hager et al. have outlined five roles for RNA to be verified experimentally to show that this transition could have occurred during evolution [127]. Four of these RNA functionalities have already been proven Its ability to specifically complex amino acids [128-132], its ability to catalyze RNA aminoacylation [106, 123, 133], acyl-transfer reactions [76, 86], amide-bond formation [76,77], and peptidyl transfer [65,66]. The remaining reaction, amino acid activation has not been demonstrated so far. 

Catalytic nucleic acids from lab to applications. Pharmacol. Rev., 52, 325. 

The second aim is selection of molecules with new catalytic function, called ribozymes. Two different approaches are used to find catalytic nucleic acids. One is to synthesize a transition-state analog (TSA) of the corresponding reaction [2], The TSA is then used as target molecule in the affinity selection scheme described above. The selected aptamers are screened to find molecules that catalyze the respective reaction that proceeds via this transition state. This concept has been successfully used for catalytic anti-... 

Since the discovery of catalytic nucleic acids and the development of methods used to generate novel species in vitro [221,222], a wide range of applications has been devised—with many implemented in an immobilized format. Like aptamers, the functionality of these nucleozymes is generally not diminished by attachment to a surface, either through affinity [223] or covalent immobilization [224], making the transition to immobilized strategies relatively straightforward. 

DNAzymes are catalytic nucleic acids capable of catalyzing a broad range of reactions such as cleaving nucleic acid substrates, ligation, and porphyrin... 

Because the intracellular Mg concentration is experimentally determined to be in the range of 0.5 mM, it would appear that the paucity of Mg would severely limit the catalytic efficiency of a DNAzyme (as well as that of a ribozyme) for the catalytic destmction of specific intracellular target mRNAs. Indeed, we have belabored this point in two previous publications, and not surprisingly others have also recognized the value of catalytic nucleic acids that could operate efficiently at low or no Mg in order to overcome this unfortunate limitation inherent to the intracellular milieu. This limitation under physiological concentrations of Mg along with an apparent absolute dependence on Mg raises questions as to the catalytic potential of DNA. 

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