Deoxyribozyme
Encyclopedia
Deoxyribozymes or DNA enzymes or catalytic DNA, or DNAzymes are DNA molecules with catalytic action. In contrast to the RNA
ribozyme
that has many catalytic capabilities, DNA is only associated with gene replication
and nothing else. The reasons are that DNA lacks specific functional group
s and that DNA prefers the double coil conformation in which potential catalytic sites are shielded. In comparison to protein
s built up from 20 different monomer
s both RNA and DNA have a much more restricted set of monomers (4) to choose from which limits the construction of interesting catalytic sites. For these reasons DNAzymes exist only in the laboratory.
at The Scripps Research Institute in La Jolla, CA. This deoxyribozyme assists in lead
ion dependent RNA cleaving operations. Catalytic amplification was found to be 100-fold compared to the uncatalysed reaction. Many other deoxyribozymes have since been developed that catalyse DNA phosphorylation, DNA adenylation
, DNA deglycosylation, porphyrin
metalation
, thymine dimer photoreversion and DNA cleavage. Of particular interest are DNA ligase
s. These molecules have demonstrated remarkable chemoselectivity
in RNA branching reactions. Although each repeating unit in a RNA strand owns a free hydroxyl
group, the DNA ligase takes just one of them as a branching starting point. An accomplishment unattainable with traditional organic chemistry
. DNAzymes have found practical use in metal biosensors.
For example, the DNA molecule 5'-GGAGAACGCGAGGCAAGGCTGGGAGAAATGTGGATCACGATT-3' which acts as a deoxyribozyme that uses light to repair a thymine dimer, using serotonin
as cofactor
.
techniques a great many DNA sequences (up to 1016 of them) can be generated in a single experiment with 20 to 200 base pair
s each, that can be screened for a specific catalytic task. In this way the sheer number of DNA candidates make up for DNA being more appropriate for information storage than for catalysis. An inherent disadvantage of DNA enzymes is product inhibition
and single-turnover behavior. It may therefore be argued if DNA enzymes can be counted as true catalysts. On the other hand low catalytic turnover is observed with many natural (non-DNA) occurring enzymes. Although the discovery of RNA enzymes predates that of DNA enzymes the latter have some distinct advantages. DNA has better cost-effectiveness
and DNA can be made with longer sequence length and can be made with higher purity in Solid-phase synthesis
.
Chirality
is another property that a DNAzyme can exploit. DNA occurs in nature as a right-handed double helix and in asymmetric synthesis a chiral catalyst is a valuable tool in the synthesis of chiral molecules from an achiral source. In one application an artificial DNA catalyst was prepared by attaching a copper ion to it through a spacer. The copper - DNA complex catalysed a Diels-Alder reaction
in water between cyclopentadiene
and an aza chalcone. The reaction products (endo and exo) were found to be present in an enantiomeric excess
of 50%. Later it was found that an enantiomeric excess of 99% could be induced, and that both the rate and the enantioselectivity were related to the DNA sequence.
Other uses of DNA in chemistry are in DNA-templated synthesis, DNA nanowires and DNA computing
.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
ribozyme
Ribozyme
A ribozyme is an RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA enzyme or catalytic RNA. Many natural ribozymes catalyze either the hydrolysis of one of their own...
that has many catalytic capabilities, DNA is only associated with gene replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
and nothing else. The reasons are that DNA lacks specific functional group
Functional group
In organic chemistry, functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction regardless of the size of the molecule it is a part of...
s and that DNA prefers the double coil conformation in which potential catalytic sites are shielded. In comparison to protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s built up from 20 different monomer
Monomer
A monomer is an atom or a small molecule that may bind chemically to other monomers to form a polymer; the term "monomeric protein" may also be used to describe one of the proteins making up a multiprotein complex...
s both RNA and DNA have a much more restricted set of monomers (4) to choose from which limits the construction of interesting catalytic sites. For these reasons DNAzymes exist only in the laboratory.
Discovery
The first deoxyribozyme was discovered in 1994 by current Yale Professor Ronald R. Breaker while a postdoctoral fellow in the laboratory of Prof. Gerald JoyceGerald Joyce
Gerald Francis Joyce is a professor and researcher at The Scripps Research Institute, best known for his work on in vitro evolution of catalytic RNA molecules and the origins of life....
at The Scripps Research Institute in La Jolla, CA. This deoxyribozyme assists in lead
Lead
Lead is a main-group element in the carbon group with the symbol Pb and atomic number 82. Lead is a soft, malleable poor metal. It is also counted as one of the heavy metals. Metallic lead has a bluish-white color after being freshly cut, but it soon tarnishes to a dull grayish color when exposed...
ion dependent RNA cleaving operations. Catalytic amplification was found to be 100-fold compared to the uncatalysed reaction. Many other deoxyribozymes have since been developed that catalyse DNA phosphorylation, DNA adenylation
Adenylation
Adenylylation is a posttranslational modification that can occur to molecules such as tyrosine residues. Adenylylation involves a phosphodiester bond between a hydroxyl group of the molecule undergoing adenylylation and the phosphate group of the adenosine monophosphate nucleotide Adenylylation is...
, DNA deglycosylation, porphyrin
Porphyrin
Porphyrins are a group of organic compounds, many naturally occurring. One of the best-known porphyrins is heme, the pigment in red blood cells; heme is a cofactor of the protein hemoglobin. Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at...
metalation
Metalation
Metalation is a chemical reaction which results in a metal atom beingattached to a molecule.Lithium metal in contact with an organohalide lithiates the organic molecule and gives the organolithium reagent and lithium halide...
, thymine dimer photoreversion and DNA cleavage. Of particular interest are DNA ligase
Ligase
In biochemistry, ligase is an enzyme that can catalyse the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group dependent to one of the larger molecules...
s. These molecules have demonstrated remarkable chemoselectivity
Chemoselectivity
Chemical reactions are defined usually in small contexts , such generalizations are a matter of utility. The preferential outcome of one instance of a generalized reaction over a set of other plausible reactions, is defined as chemoselectivity...
in RNA branching reactions. Although each repeating unit in a RNA strand owns a free hydroxyl
Hydroxyl
A hydroxyl is a chemical group containing an oxygen atom covalently bonded with a hydrogen atom. In inorganic chemistry, the hydroxyl group is known as the hydroxide ion, and scientists and reference works generally use these different terms though they refer to the same chemical structure in...
group, the DNA ligase takes just one of them as a branching starting point. An accomplishment unattainable with traditional organic chemistry
Organic chemistry
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, composition, reactions, and preparation of carbon-based compounds, hydrocarbons, and their derivatives...
. DNAzymes have found practical use in metal biosensors.
For example, the DNA molecule 5'-GGAGAACGCGAGGCAAGGCTGGGAGAAATGTGGATCACGATT-3' which acts as a deoxyribozyme that uses light to repair a thymine dimer, using serotonin
Serotonin
Serotonin or 5-hydroxytryptamine is a monoamine neurotransmitter. Biochemically derived from tryptophan, serotonin is primarily found in the gastrointestinal tract, platelets, and in the central nervous system of animals including humans...
as cofactor
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....
.
Usage
With the aid of combinatorial chemistryCombinatorial chemistry
Combinatorial chemistry involves the rapid synthesis or the computer simulation of a large number of different but structurally related molecules or materials...
techniques a great many DNA sequences (up to 1016 of them) can be generated in a single experiment with 20 to 200 base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
s each, that can be screened for a specific catalytic task. In this way the sheer number of DNA candidates make up for DNA being more appropriate for information storage than for catalysis. An inherent disadvantage of DNA enzymes is product inhibition
Enzyme inhibitor
An enzyme inhibitor is a molecule that binds to enzymes and decreases their activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used as herbicides and pesticides...
and single-turnover behavior. It may therefore be argued if DNA enzymes can be counted as true catalysts. On the other hand low catalytic turnover is observed with many natural (non-DNA) occurring enzymes. Although the discovery of RNA enzymes predates that of DNA enzymes the latter have some distinct advantages. DNA has better cost-effectiveness
Cost-effectiveness
Cost-effectiveness analysis is a form of economic analysis that compares the relative costs and outcomes of two or more courses of action. Cost-effectiveness analysis is distinct from cost-benefit analysis, which assigns a monetary value to the measure of effect...
and DNA can be made with longer sequence length and can be made with higher purity in Solid-phase synthesis
Solid-phase synthesis
In chemistry, solid-phase synthesis is a method in which molecules are bound on a bead and synthesized step-by-step in a reactant solution; compared with normal synthesis in a liquid state, it is easier to remove excess reactant or byproduct from the product. In this method, building blocks are...
.
Chirality
Chirality (chemistry)
A chiral molecule is a type of molecule that lacks an internal plane of symmetry and thus has a non-superimposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom....
is another property that a DNAzyme can exploit. DNA occurs in nature as a right-handed double helix and in asymmetric synthesis a chiral catalyst is a valuable tool in the synthesis of chiral molecules from an achiral source. In one application an artificial DNA catalyst was prepared by attaching a copper ion to it through a spacer. The copper - DNA complex catalysed a Diels-Alder reaction
Diels-Alder reaction
The Diels–Alder reaction is an organic chemical reaction between a conjugated diene and a substituted alkene, commonly termed the dienophile, to form a substituted cyclohexene system. The reaction can proceed even if some of the atoms in the newly formed ring are not carbon...
in water between cyclopentadiene
Cyclopentadiene
Cyclopentadiene is an organic compound with the formula C5H6. This colorless liquid has a strong and unpleasant odor. At room temperature, this cyclic diene dimerizes over the course of hours to give dicyclopentadiene via a Diels–Alder reaction...
and an aza chalcone. The reaction products (endo and exo) were found to be present in an enantiomeric excess
Enantiomeric excess
The enantiomeric excess of a substance is a measure of how pure it is. In this case, the impurity is the undesired enantiomer .-Definition:...
of 50%. Later it was found that an enantiomeric excess of 99% could be induced, and that both the rate and the enantioselectivity were related to the DNA sequence.
Other uses of DNA in chemistry are in DNA-templated synthesis, DNA nanowires and DNA computing
DNA computing
DNA computing is a form of computing which uses DNA, biochemistry and molecular biology, instead of the traditional silicon-based computer technologies. DNA computing, or, more generally, biomolecular computing, is a fast developing interdisciplinary area...
.