Deoxyribozyme

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... 

Cleavage in the presence of histidine releases the oligonucleotide fragment containing the random sequence, and this is amplified by PCR and the cycle repeated. This selection procedure produced deoxyribozymes that require no metal cofactor but have a specific requirement for L-histidine, which is presumed (from pH-rate profiles) to act as a general... 

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. 

A new dimension in the development of nucleic acid based catalysts was introduced by Breaker and Joyce in 1994 when they isolated the first deoxyribozyme [111]. It is not unexpected that DNA is also able to catalyze chemical reactions because it was shown previously that ssDNA aptamers which bind to a variety of ligands can be isolated by in vitro selection [141]. In the meantime, several deoxyribozymes have been described which expand the range of chemical transformations accelerated by nucleic acid catalysts even further and raising question whether even catalytic DNA might have played some role in the pre-biotic evolution of hfe on earth [69-71]. 

After five cycles of selection and ampHfication, a population of single-stranded DNAs was enriched that catalyzed the Pb +-dependent cleavage at the ribose residue. This intramolecular cleavage activity was transformed into an inter-molecular reaction by separating the 38-nucleotide long catalytic domain from the 21-mer substrate which was cleaved specifically and with high turnover rates. Remarkably, the deoxyribozyme can perform well only with the special DNA/RNA chimeric oHgonucleotide substrate and cannot cleave a pure RNA substrate of the same sequence. 

This goal was recently achieved by Santoro and Joyce who isolated a deoxyribozyme which is able to hybridize to and cleave any RNA sequence under phy-... 

Fig. 13. The deoxyribozyme bottom strand) hybridizes to the RNA substrate oligonucleotide top strand). The site of cleavage is indicated by the arrow (R = A or G Y = U or C). The sequences of the helical parts of the enzyme can be chosen as desired, so that almost any RNA sequence can be targeted by the catalytic DNA...

Meanwhile other experiments have been carried out to isolate DNA molecules with either RNA- or DNA-phosphoesterase activity [69-71,142,143]. Since Mg +-dependent rather than Pb +-dependent cleavage is compatible with intracellular conditions and thus, more suitable for possible medical applications, deoxyribozymes were selected that used Mg + instead of Pb for cleavage [112]. One optimized deoxyribozyme that emerged in this selection showed a cleavage rate of 0.01 min and was also capable of intermolecular cleavage. 

To develop deoxyribozymes that make use of a non-metal cofactor rather than divalent metal ions for the cleavage of a ribonucleotide residue we performed an in vitro selection under conditions of low magnesium concentration, or... 

Another class of cofactor-dependent deoxyribozymes that use the amino acid histidine to promote phosphodiester cleavage was isolated recently by Roth and Breaker [113]. One of the isolated DNA requires L-histidine or a closely related analog to support RNA phosphodiester cleavage with a rate enhancement of nearly a million-fold over the basal substrate cleavage rate (Fig. 14). 

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]. 

Silverman, S. K. (2008). Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects. Chem. Commun. (Camb.) 14(30), 3467—3485. 

Baum, DanaA., and Scott, K. S. (2007). Deoxyribozyme-catalyzedlabeling ofRNA. Angew. Chem. 46, 3502-3504. 

Further efforts needed to develop deoxyribozymes for linear... 

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