DNA-based catalysis

Fig. 1 The three approaches to DNA-based catalysis described in this chapter...

Fig. 12 Concept of DNA-based catalysis in the noncovalent approach. A Class 1 ligands. B-D Class 2 ligands...

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). 

Fig. 15 a, b Phosphine-modified oligonucleotides used in the covalent approach towards DNA-based catalysis... 

En me Mechanism. Staphylococcal nuclease (SNase) accelerates the hydrolysis of phosphodiester bonds in nucleic acids (qv) some 10 -fold over the uncatalyzed rate (r93 and references therein). Mutagenesis studies in which Glu43 has been replaced by Asp or Gin have shown Glu to be important for high catalytic activity. The enzyme mechanism is thought to involve base catalysis in which Glu43 acts as a general base and activates a water molecule that attacks the phosphodiester backbone of DNA. To study this mechanistic possibiUty further, Glu was replaced by two unnatural amino acids. 

The experimentally observed pseudo-first order rate constant k is increased in the presence of DNA (18,19). This enhanced reactivity is a result of the formation of physical BaPDE-DNA complexes the dependence of k on DNA concentration coincides with the binding isotherm for the formation of site I physical intercalative complexes (20). Typically, over 90% of the BaPDE molecules are converted to tetraols, while only a minor fraction bind covalently to the DNA bases (18,21-23). The dependence of k on temperature (21,24), pH (21,23-25), salt concentration (16,20,21,25), and concentration of different buffers (23) has been investigated. In 5 mM sodium cacodylate buffer solutions the formation of tetraols and covalent adducts appear to be parallel pseudo-first order reactions characterized by the same rate constant k, but different ratios of products (21,24). Similar results are obtained with other buffers (23). The formation of carbonium ions by specific and general acid catalysis has been assumed to be the rate-determining step for both tetraol and covalent adduct formation (21,24). 

Roelfes, G. and Feringa, B.L. (2005) DNA-based asymmetric catalysis. Angew. Chem., Int. Ed., 44, 3230-3232 Kraemer, R. (2006) Supramolecular bioinorganic hybrid catalysts for enantioselective transformations. Angew. Chem., Int. Ed., 45, 858-860. 

Catalytic antibodies, like enzymes, must be isolated and purified to homogeneity before they can be studied. Initially this was done by using the hybridoma technique for isolation of monoclonal antibodies (Box 31-A). After induction of antibody formation by injecting a selected hapten into a mouse, large numbers of monoclonal antibodies had to be tested for catalytic activity. Even if several thousand different monoclonal antibodies were tested, only a few with catalytic properties could be found.1 Newer methods have incorporated recombinant DNA techniques (Box 31-A) and use of combinatorial libraries and phage display.) Incorporation of acidic or basic groups into the haptens used to induce antibody formation may yield antibodies capable of mimicking the acid-base catalysis employed by natural enzymes. 0... 

According to the above scheme, there is a branching into a base propenal and malonaldehyde [reactions (30) and (31)]. In the radiolysis of DNA in aqueous solution, malonaldehyde is formed (see below), but there are practically no base propenals. On the other hand, in BLM-treated DNA, base propenals dominate. If these two products have the same precursor as in the above scheme, BLM still bound to DNA must catalyze reaction (30), while without this catalysis, reaction (31) must predominate. Experiments that could elucidate this point have not yet been carried out. 

Roelfes s supramolecular assembly is one of the most efficient enan-tioselective catalysts for aqueous Michael additions. The DNA template approach has also been used for enantioselective Friedel-Crafts reactions in water, with outstanding results in terms of conversion and enantioselectivities (110). All these results confirm the impressive potential of DNA-based enantioselective catalysis. 

Recently, a controversial debate has arisen about whether the optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of tunneling and thereby accelerate reaction rates [7]. Kinetic isotope effect experiments have indicated that hydrogen tunneling plays an important role in many proton and hydride transfer reactions in enzymes [8, 9]. Enzyme catalysis of horse liver alcohol dehydrogenase may be understood by a model of vibrationally enhanced proton transfer tunneling [10]. Furthermore, the double proton transfer reaction in DNA base pairs has been studied in detail and even been hypothesized as a possible source of spontaneous mutation [11-13]. 

Since DNA is stable under the same conditions, the 2 -hydroxyl is likely to have some catalytic role but this role is not obvious. The hydroxyl group is a poor Bronsted acid or base. Reactions at unactivated phosphorus are not subject to significant general acid or base catalysis. Therefore another mechanism must be operative. 

The very special properties of DNA, one of the icons of modem science, make it one of the most versatile molecules in chemistry. In nature, it serves as the carrier of genetic information and as such is one of the cornerstones of life [1]. In vitro, a very diverse set of applications have been explored, ranging from programmable building blocks in bionanotechnology [2] to scaffolds for catalysis. In this review, we will focus on this last aspect, with a particular emphasis on metal catalysis. Three approaches will be discussed DNAzymes, DNA-templated catalysis, and DNA-based asymmetric catalysis (Fig. 1). Artificial DNA-metal base pairing [3] will not be covered, as no catalysis using these systems has been reported to date. 

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