Oligonucleotide catalysts

For a poly- or oligonucleotide catalyst-substrate interaction the problem of binding-specificity is in principle solved simply by using the complementary sequence, and chemistry based on classical... 

As an application of an oligonucleotide catalyst, we immobilized DNAzyme carrying peroxidase activity with hemin on gold particles using a thiol modification of the DNAzyme s end to detect peroxide 116). Usually, horseradish peroxidase is immobilized on a solid support. Compared with protein enzymes, the DNAzyme is advantageous because of its thermal stability and convenience of preparation. 

Synthetic organic polymers, which are used as polymeric supports for chromatography, as catalysts, as solid-phase supports for peptide and oligonucleotide synthesis, and for diagnosis, are based mainly on polystyrene, polystyrene-divinylbenzene, polyacrylamide, polymethacrylates, and polyvinyl alcohols. A conventional suspension of polymerization is usually used to produce these organic polymeric supports, especially in large-scale industrial production. 

While many diseases have long been known to result from alterations in an individual s DNA, tools for the detection of genetic mutations have only recently become widely available. These techniques rely upon the catalytic efficiency and specificity of enzyme catalysts. For example, the polymerase chain reaction (PCR) relies upon the ability of enzymes to serve as catalytic amplifiers to analyze the DNA present in biologic and forensic samples. In the PCR technique, a thermostable DNA polymerase, directed by appropriate oligonucleotide primers, produces thousands of copies of a sample of DNA that was present initially at levels too low for direct detection. 

Although the pre-RNA world is now much more the centre of scientific attention in prebiotic chemistry, there have been several attempts in recent years to understand the synthesis of oligonucleotides from the normal nucleotides by using simulation experiments (Ferris, 1998). In condensation reactions in aqueous media, there is always competition between synthesis and hydrolysis synthesis is generally only successful when supported by catalysts. 

The enzymatic activity of the L-19 IVS ribozyme results from a cycle of transesterification reactions mechanistically similar to self-splicing. Each ribozyme molecule can process about 100 substrate molecules per hour and is not altered in the reaction therefore the intron acts as a catalyst. It follows Michaelis-Menten kinetics, is specific for RNA oligonucleotide substrates, and can be competitively inhibited. The kcat/Km (specificity constant) is 10s m- 1 s lower than that of many enzymes, but the ribozyme accelerates hydrolysis by a factor of 1010 relative to the uncatalyzed reaction. It makes use of substrate orientation, covalent catalysis, and metalion catalysis—strategies used by protein enzymes. 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

Another possible electrocatalytic process is that related to a surface-bound molecule which can give rise to a two-electron reaction. In these conditions, the coupling of the catalytic reaction in the presence of an adequate species in solution can lead to different mechanistic schemes from which the elucidation of the global reaction path is not immediate. This situation matches the behavior of a great number of inorganic catalysts (such polyoxometallates or ion complexes) [86, 98] and biological molecules (enzymes, proteins, oligonucleotides, etc.) [79, 80], for which there is a lack of theoretical basis which enables a clear classification of the different possibilities that can be encountered. 

Metal-free catalysts for the hydrolysis of RNA derived from 2-aminobenzimidazoles were reported. The most active catalysts, tris derivatives (99 R = H, CC Me) built upon a framework of tris(2-aminoethyl)amine, were shown by fluorescence correlation spectroscopy to aggregate with oligonucleotides. However, at very low concentrations the compounds were still active in the non-aggregated state. Conjugates of the ester (99 CC Me) with antisense oligonucleotides or RNA binding peptides will, it was claimed, be promising candidates as site specific artificial ribonucleases.98... 

Enhanced electrochemical signals for DNA can be obtained by catalytic electrochemical oxidation using transition metal complexes/341 Studies by Thorp et al/35 01 showed that Ru(bpy)f+ (bpy=2,2 -bipyridine) is an efficient electrochemical catalyst that oxidizes only guanine bases in DNA and oligonucleotides. The reaction follows the catalytic pathway below ... 

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