DNA catalysts

Catalytic DNA is made possible because single-stranded DNA can adopt complex tertiary structures in a similar way to RNA, although unlike RNA no DNA-based catalysts have yet been found in nature. Both DNA aptamers and DNA catalysts (deoxyribozymes) can be... 

Silverman, S. K. (2004). Deoxyribozymes DNA catalysts for bioorganic chemistry. Org Biomol Chem 2, 2701-2706. 

In future, this might be achieved by the introduction of photocleavable linker molecules to remove large residues prior to PCR amplification [175]. Thus, various chemical moieties such as aromatic residues, amino acids or lipid modifications could be introduced in nucleic acid libraries by this method, allowing rapid access to modified libraries for aptamer selection and the selection of novel DNA catalysts. 

Heterogeneous reaction (Section 6 1) A reaction involving two or more substances present in different phases Hydro genation of alkenes is a heterogeneous reaction that takes place on the surface of an insoluble metal catalyst Heterolytic cleavage (Section 4 16) Dissociation of a two electron covalent bond in such a way that both electrons are retained by one of the initially bonded atoms Hexose (Section 25 4) A carbohydrate with six carbon atoms High density lipoprotein (HDL) (Section 26 11) A protein that carries cholesterol from the tissues to the liver where it is metabolized HDL is often called good cholesterol Histones (Section 28 9) Proteins that are associated with DNA in nucleosomes... 

Although, as stated above, we wiU mostly focus on hydrolytic systems it is worth discussing oxidation catalysts briefly [8]. Probably the best known of these systems is exemphfied by the antitumor antibiotics belonging to the family of bleomycins (Fig. 6.1) [9]. These molecules may be included in the hst of peptide-based catalysts because of the presence of a small peptide which is involved both in the coordination to the metal ion (essential co-factor for the catalyst) and as a tether for a bisthiazole moiety that ensures interaction with DNA. It has recently been reported that bleomycins will also cleave RNA [10]. With these antibiotics DNA cleavage is known to be selective, preferentially occurring at 5 -GpC-3 and 5 -GpT-3 sequences, and results from metal-dependent oxidation [11]. Thus it is not a cleavage that occurs at the level of a P-O bond as expected for a non-hydrolytic mechanism. 

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 use of rihozymes and DNA-zymes is hmited to the field of nucleic acid transformations, with small exceptions only that concern their use as catalysts in the Diels-Alder cycloaddition, a strong interest to use them in the stereoselective synthesis of heteroatom compounds can be expected. 

The above two processes employ isolated enzymes - penicillin G acylase and thermolysin, respectively - and the key to their success was an efficient production of the enzyme. In the past this was often an insurmountable obstacle to commercialization, but the advent of recombinant DNA technology has changed this situation dramatically. Using this workhorse of modern biotechnology most enzymes can be expressed in a suitable microbial host, which enables their efficient production. As with chemical catalysts another key to success often is the development of a suitable immobilization method, which allows for efficient recovery and recycling of the biocatalyst. 

Recently, Li et al. have reported an efficient 1,3-dipolar cycloaddition of azides with electron-deficient alkynes without any catalysts at room temperature in water.128 The reaction has been applied successfully to the coupling of an azido-DNA molecule with electron-deficient alkynes for the formation of [l,2,3]-triazole heterocycle (Eq. 4.66). 

We first consider the stmcture of the rate constant for low catalyst densities and, for simplicity, suppose the A particles are converted irreversibly to B upon collision with C (see Fig. 18a). The catalytic particles are assumed to be spherical with radius a. The chemical rate law takes the form dnA(t)/dt = —kf(t)ncnA(t), where kf(t) is the time-dependent rate coefficient. For long times, kf(t) reduces to the phenomenological forward rate constant, kf. If the dynamics of the A density field may be described by a diffusion equation, we have the well known partially absorbing sink problem considered by Smoluchowski [32]. To determine the rate constant we must solve the diffusion equation... 

Chiral recognition of A-[Co(phen)3]3+ has been observed in a modified /3-cyclodextrin.772 Chiral discrimination has also been seen in photoinduced energy transfer from luminescent chiral lanthanoid complexes773 to [Co(phen)3]3+ and between photoexcited [Ru(bpy)3]2+ and [Co(phen)3]3+ co-adsorbed on smectite clays.774 The [Co(bpy)3]3+ ion has been incorporated into clays to generate ordered assemblies and also functional catalysts. When adsorbed onto hectorite, [Co(bpy)3]3+ catalyzes the reduction of nitrobenzene to aniline.775 The ability of [Co(phen)3]3+ to bind to DNA has been intensively studied, and discussion of this feature is deferred until Section 6.1.3.1.4. 

Although the systems described here have not been used for nanoencapsulated cascade reactions, or of course, for mutually incompatible catalysts, they offer an attractive possibility for the extension of this field, especially given the availability of a wide range of protein-based nanometer-sized cages, such as chaperonins, DNA binding proteins, and the extensive class of viruses [107]. 

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