Ribozymes deoxyribozymes

Peracchi A (2004) Prospects for antiviral ribozymes and deoxyribozymes. Rev Med Virol 14 47-64 Petersen M, Wengel J (2003) LNA a versatile tool for therapeutics and genomics. Trends Biotech-nol 21 74-81... 

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]. 

The only indirect selection that led to a catalytic DNA is a deoxyribozyme that catalyzes the same class of porphyrin metallation as the aforementioned ribozyme. The ssDNA oligonucleotide showed a k at of 13 h" for the insertion of into mesoporphyrin IX [93, 96-99]. This corresponds to a rate enhancement of 1400 compared to the uncatalyzed reaction which is as good as a catalytic antibody for the same reaction. 

Bm-gstaUer P, Famulok M (1998) Synthetic ribozymes and deoxyribozymes, in press. In Waldmann H, Mulzer J (ed) Organic Synthesis Highhghts, vol 3. Wiley-VCH, Weinheim... 

Aptamers are nucleic acids which exhibit a defined structure due to their nucleotide sequence and therefore, are able to specifically bind selected targets [1] (aptus [lat.] = fitting, sticking to). Aptamers and likewise, ribozymes [2] and deoxyribozymes [3] are selected in vitro by screening nucleic acid libraries. Here we describe in detail the selection of aptamers by a process called SELEX (Systematic Evolution of Ligands by Exponential enrichment) [4]. 

Figure 5.1 Deoxyribozyme-catalyzed RNA cleavage. (A) The cleavage reaction, which forms 2,3,-cyclic phosphate and 5-OH RNA termini. (B) Individual deoxy-ribozymes and their target sequences for efficient cleavage of all-RNA substrates. N, any nucleotide R, purine Y, pyrimidine. Outside of the expheidy indicated nucleotides, any RNA sequence is tolerated as long as Watson-Crick RNA DNA covariation is maintained.

Figure 5.5 Individual deoxyribozymes for branched RNA synthesis. (A) 7S11 deoxy-ribozyme. Note the four Watson-Crick paired regions denoted P1-P4. (B) 10DM24 deoxyribozyme. (C) 6CE8 deoxyribozyme. (D) 6BX22 deoxyribozyme.

Paul, N., Springsteen, G., and Joyce, G. F. (2006). Conversion of a ribozyme to a deoxyribozyme through in vitro evolution. Chem. Biol. 13, 329-338. 

Silverman, S. K. (2009). Artificial functional nucleic acids Aptamers, ribozymes, and deoxyribozymes identified by in vitro selection. In Functional Nucleic Acids for Analytical Applications, (Y. Li and Y. Lu, eds.), pp. 47-108. Springer Science+Business Media, LLC, New York. 

There are fewer catalytic ribozymes compared to deoxyribozymes. Examples... 

Alessio Peracchi obtained a degree in veterinary medicine from the University of Parma in 1989, and later a Ph.D. in molecular biotechnology at the Catholic University of the Sacred Heart, Piacenza, Italy in 1994, and conducted postdoctoral research at Stanford University. In 1998, he became a permanent researcher at the University of Parma, and since 2000 he is an associate professor of biochemistry at the same institution. In 2001, he was nominated EMBO Young Investigator by the European Molecular Biology Organization. His research centers on the function and evolution of catalytic biomacromolecules, contributing to the field with studies on protein enzymes, ribozymes, and deoxyribozymes (catalytic DNAs). 

Schubert S, Kurreck J (2004). Ribozyme- and deoxyribozyme-strategies for medical applications. Curr. Drug Targets. 5 667-681. 

Nucleic acids Ribozymes (catalytic RNA) and deoxyribozymes (catalytic DNA)... 

Some nucleic acids are capable of self-splicing. These catalytic DNA and RNA are known as deoxyribozymes (Li and Breaker, 1999 Sheppard et al, 2000) and ribozymes (Doherty and Doudna, 2000 Scott and Klug, 1996) respectively. The 3 - and/or 2 -hydroxyls of DNA/RNA serve as a catalytic site that invariably requires a metal ion for the catalytic activity. Deoxyribozymes are quasi-catalytic while ribozymes can be catalytic, e.g. ribonuclease P (RNase P) as well as quasi-catalytic, e.g. introns and hammerhead RNAs. RNase P resources are maintained at http //www.mbio.ncsu.edu/RnaseP/homeJitml... 

S. M. Knudsen, A. D. Ellington. Aptazymes Allosteric Ribozymes and Deoxyribozymes as Biosensors, in The Aptamer Handbook, S. Klussmann (Ed.), Wiley-VCH, Weinheim, 290-310, 2006. 

Upper Limits of a Degenerate DNA Synthesis - A Cap on Outcome Catalytic RNA Cleavage by Ribozymes and DNAzymes DNAzymes - Deoxyribozymes M -lndependent RNA-Cleaving DNAs... 

There are fewer catalytic ribozymes compared to deoxyribozymes. Examples include a trara-splicing ribozyme, an alcohol dehydrogenase, a ligase capable of functioning at low temperature, " a ribozyme that will ligate the 5 -terminus of RNA to a polypeptide, a transcriptional activator and a tRNA aminoacylation catalyst. An RNA aptamer bearing 5 -CoA has been selected to catalyse thioester formation in the presence of biotin-AMP. In vitro selection has also been used to identify allosteric hairpin ribozymes, activated in the presence of short oligonucleotides, and a ribozyme that catalyses amide bond formation from a 2 -amino nucleotide. " ... 

In vitro selection methods permit the generation of ribozymes and deoxyribozymes (catalytic DNA) with allosteric properties, wherein the binding of an effector molecule controls the catalytic function. This feature provides challenging opportunities for the development of new analytical and very specific tools using traditional assay formats or for the development of entirely new biosensing principles. 

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