DNA-directed catalysis

DNA-directed catalysis was first reported by Vlassov and coworkers [103], who attached EDTA covalently to octathymidylate and showed that the modified ohgo-nucleotide in the presence of Fe and dithiothreitol (DTT) cleaved poly(A) and 

The concept of DNA-directed catalysis has been applied to many metal binding ligands other than EDTA, giving rise to catalysts capable of oxidative and/or hydrolytic cleavage of polynncleotide snbstrates. 

Although iron-bleomycin itself is well known for its sequence-specific ds-DNA cleaving abilities, it was also covalently bound to oligonucleotides, leading to cleavage of DNA [119], with the capability of performing multiple turnovers when 

Other ligands incorporated into oligonncleotides that showed cleavage activity npon addition of metal ions inclnde bpy (2,2 -bipyridine) [ 122-124], tpy (2,2 6, 2 -terpyridine) [122,124-127], and 2,6-dicarboxypicoline or AA -bis(2-picolyl)amine [128, 129]. 

An intruiging approach to site-selective RNA cleavage was reported by Kuzuya et al. [130]. In contrast to the previons examples, in this system the metal complex is free in solution (not localized). Site-selective activation for hydrolysis at single positions in a target RNA strand is achieved by covalent attachment of an acridine moiety to the template DNA strand, which canses local perturbation in the hybridized RNA strand opposite this position [131]. RNA strand scission is very site-specific for the localized perturbation (Fig. 9b). This approach was optimized for various metal ions inclnding Ca and Mg % transition metal ions, and lanthanide ions [132, 133]. Two sites in a single RNA conld be activated by incorporation of two acridines in the DNA template [134], and the rate of the process was further enhanced by the attachment of a ligand for Lu in close proximity to the acridine activator [135]. 

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Fig. 8 Schematic representation of the concepts of DNA-directed catalysis (a) and DNA-templated catalysis (b)...

The covalent approach towards DNA-based catalysis involves direct attachment of the catalytically active metal complex to the DNA via a covalent bond. The presumed advantage of this approach over the supramolecular variant is the greater control over both the geometry around the metal center and the exact microenvironments (i.e., the DNA sequence) in which the metal complex is located. So far, two reports have been published in which transition metals were anchored to deoxyribonucleotides via covalently linked phosphine ligands (Fig. 15). 

This chapter has presented an overview of applications of DNA in metal ion catalysis. Three general approaches were outlined metal-dependent DNAzymes, DNA-directed and templated catalysis, and DNA-based asymmetric catalysis. 

Figure 13.8 Proposed reaction mechanism for DNA polymerase catalysis. The polymerase active site contains three carhoxylate residues and probably a lysine. The three carboxylate side chains anchor a pair of divalent metal ions (e.g. Mg ). In the proposed mechanism, two carboxy-lates coordinate directly to the two Mg, one of which promotes the deprotonation of the 3 -OH of the primer. An in-hne attack of the a-phosphorus atom of dNTP forms a bipyramidal pentaco-ordinated oxyphosphorane transition state with the in-coming and departing atoms at apical positions. The possible involvement of a third Mg coordinated to P- and y-phosphates is also shown...

Secheresse reported size-controlled formation of silver nanparticles (43) by direct bonding of ruthenium complex 42 and silver nanoparticles. Oxazole 42 was formed by the reaction of diketone 40 and aldehydes 41 under the influence of NH4OAC. These metallic nanoparticles may find applications in DNA sequencing, catalysis, optics, nanoscale electronics and antimicrocrobials. ... 

DNA polymerases catalyze DNA synthesis in a template-directed manner (Box 16). For most known DNA polymerases a short DNA strand hybridized to the template strand is required to serve as a primer for initiation of DNA synthesis. Nascent DNA synthesis is promoted by DNA polymerases by catalysis of nucleophilic attack of the 3 -hydroxyl group of the 3 -terminal nucleotide of the primer strand on the a-phosphate of an incoming nucleoside triphosphate (dNTP), leading to substitution of pyrophosphate. This phosphoryl transfer step is promoted by two magnesium ions that stabilize a pentacoordinated transition state by complex-ation of the phosphate groups and essential carboxylate moieties in the active site (Figure 4.1.1) [2],... 

The following new trends in enzymatic synthesis can be delineated the development of new enzymatic reactions enzyme immobilization and stabilization the use of organic solvents and two phase systems site-directed mutagenesis chemical modification of enzymes antibody catalysis catalysis by RNA and DNA de novo design ofbiocatalists employment of recombinant DNA for production of enzymes and use computational and combinatorial methods... 

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