Deoxyribozyme

Last updated

Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a specific chemical reaction, often but not always catalytic. This is similar to the action of other biological enzymes, such as proteins or ribozymes (enzymes composed of RNA). [1] However, in contrast to the abundance of protein enzymes in biological systems and the discovery of biological ribozymes in the 1980s, [2] [3] there is only little evidence for naturally occurring deoxyribozymes. [4] [5] Deoxyribozymes should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but do not catalyze a subsequent chemical reaction.

Contents

With the exception of ribozymes, nucleic acid molecules within cells primarily serve as storage of genetic information due to its ability to form complementary base pairs, which allows for high-fidelity copying and transfer of genetic information. In contrast, nucleic acid molecules are more limited in their catalytic ability, in comparison to protein enzymes, to just three types of interactions: hydrogen bonding, pi stacking, and metal-ion coordination. This is due to the limited number of functional groups of the nucleic acid monomers: while proteins are built from up to twenty different amino acids with various functional groups, nucleic acids are built from just four chemically similar nucleobases. In addition, DNA lacks the 2'-hydroxyl group found in RNA which limits the catalytic competency of deoxyribozymes even in comparison to ribozymes. [6]

In addition to the inherent inferiority of DNA catalytic activity, the apparent lack of naturally occurring deoxyribozymes may also be due to the primarily double-stranded conformation of DNA in biological systems which would limit its physical flexibility and ability to form tertiary structures, and so would drastically limit the ability of double-stranded DNA to act as a catalyst; [6] though there are a few known instances of biological single-stranded DNA such as multicopy single-stranded DNA (msDNA), certain viral genomes, and the replication fork formed during DNA replication. Further structural differences between DNA and RNA may also play a role in the lack of biological deoxyribozymes, such as the additional methyl group of the DNA base thymidine compared to the RNA base uracil or the tendency of DNA to adopt the B-form helix while RNA tends to adopt the A-form helix. [1] However, it has also been shown that DNA can form structures that RNA cannot, which suggests that, though there are differences in structures that each can form, neither is inherently more or less catalytic due to their possible structural motifs. [1]

In 2021, the DNAmoreDB database for cataloguing known deoxyribozymes was released. [7]

Types

Ribonucleases

The trans-form (two separate strands) of the 17E DNAzyme. Most ribonuclease DNAzymes have a similar form, consisting of a separate enzyme strand (blue/cyan) and substrate strand (black). Two arms of complementary bases flank the catalytic core (cyan) on the enzyme strand and the single ribonucleotide (red) on the substrate strand. The arrow shows the ribonucleotide cleavage site. 17E (Pb2+-selective) DNAzyme.png
The trans-form (two separate strands) of the 17E DNAzyme. Most ribonuclease DNAzymes have a similar form, consisting of a separate enzyme strand (blue/cyan) and substrate strand (black). Two arms of complementary bases flank the catalytic core (cyan) on the enzyme strand and the single ribonucleotide (red) on the substrate strand. The arrow shows the ribonucleotide cleavage site.

The most abundant class of deoxyribozymes are ribonucleases, which catalyze the cleavage of a ribonucleotide phosphodiester bond through a transesterification reaction, forming a 2'3'-cyclic phosphate terminus and a 5'-hydroxyl terminus. [6] [8] Ribonuclease deoxyribozymes typically undergo selection as long, single-stranded oligonucleotides which contain a single ribonucleotide base to act as the cleavage site. Once sequenced, this single-stranded "cis"-form of the deoxyribozyme can be converted to the two-stranded "trans"-form by separating the substrate domain (containing the ribonucleotide cleavage site) and the enzyme domain (containing the catalytic core) into separate strands which can hybridize through two flanking arms consisting of complementary base pairs.

The first known deoxyribozyme was a ribonuclease, discovered in 1994 by Ronald Breaker while a postdoctoral fellow in the laboratory of Gerald Joyce at the Scripps Research Institute. [9] This deoxyribozyme, later named GR-5, [10] catalyzes the Pb2+-dependent cleavage of a single ribonucleotide phosphoester at a rate that is more than 100-fold compared to the uncatalyzed reaction. [9] Subsequently, additional RNA-cleaving deoxyribozymes that incorporate different metal cofactors were developed, including the Mg2+-dependent E2 deoxyribozyme [11] and the Ca2+-dependent Mg5 deoxyribozyme. [12] These first deoxyribozymes were unable to catalyze a full RNA substrate strand, but by incorporating the full RNA substrate strand into the selection process, deoxyribozymes which functioned with substrates consisting of either full RNA or full DNA with a single RNA base were both able to be utilized. [13] The first of these more versatile deoxyribozymes, 8-17 and 10–23, are currently the most widely studied deoxyribozymes. In fact, many subsequently discovered deoxyribozymes were found to contain the same catalytic core motif as 8–17, including the previously discovered Mg5, suggesting that this motif represents the "simplest solution for the RNA cleavage problem". [8] [14] The 10-23 DNAzyme contains a 15-nucleotide catalytic core that is flanked by two substrate recognition domains. This DNAzyme cleaves complementary RNAs efficiently in a sequence specific manner between an unpaired purine and a paired pyrimidine. DNAzymes targeting AU or GU vs. GC or AC are more effective. Furthermore, the RNA cleavage rates have been shown to increase after the introduction of intercalators or the substitution of deoxyguanine with deoxyinosine at the junction of the catalytic loop. Specifically, the addition of 2’-O-methyl modifications to the catalytic proved to significantly increase the cleavage rate both in vitro and in vivo. [15] Additionally, recent studies have focuses on unravelling their kinetics to further understand their performance. [16] Other notable deoxyribozyme ribonucleases are those that are highly selective for a certain cofactor. Among this group are the metal selective deoxyribozymes such as Pb2+-specific 17E, [17] UO22+-specific 39E, [18] and Na+-specific A43. [19] First crystal structure of a DNAzyme was reported in 2016. [20] [21] 10-23 core based DNAzymes and the respective MNAzymes that catalyse reactions at ambient temperatures were described in 2018 [22] and open doors for use of these nucleic acid based enzymes for many other applications without the need for heating.

A DNA molecule with sequence 5'-GGAGAACGCGAGGCAAGGCTGGGAGAAATGTGGATCACGATT-3' acts as a deoxyribozyme that uses light to repair a thymine dimer, using serotonin as cofactor. [23]

RNA ligases

Of particular interest are DNA ligases. [6] 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. This cannot be done with traditional organic chemistry.

Other reactions

Many other deoxyribozymes have since been developed that catalyze DNA phosphorylation, DNA adenylation, DNA deglycosylation, porphyrin metalation, thymine dimer photoreversion [24] and DNA cleavage.

Methods

in vitro selection

Because there are no known naturally occurring deoxyribozymes, most known deoxyribozyme sequences have been discovered through a high-throughput in vitro selection technique, similar to SELEX. [25] [26] in vitro selection utilizes a "pool" of a large number of random DNA sequences (typically 1014–1015 unique strands) that can be screened for a specific catalytic activity. The pool is synthesized through solid phase synthesis such that each strand has two constant regions (primer binding sites for PCR amplification) flanking a random region of a certain length, typically 25–50 bases long. Thus the total number of unique strands, called the sequence space, is 4N where N denotes the number of bases in the random region. Because 425 ≈ 1015, there is no practical reason to choose random regions of less than 25 bases in length, while going above this number of bases means that the total sequence space cannot be surveyed. However, since there are likely many potential candidates for a given catalytic reaction within the sequence space, random regions of 50 and even higher have successfully yielded catalytic deoxyribozymes. [26]

The pool is first subjected to a selection step, during which the catalytic strands are separated from the non-catalytic strands. The exact separation method will depend on the reaction being catalyzed. As an example, the separation step for ribonucleotide cleavage often utilizes affinity chromatography, in which a biological tag attached to each DNA strand is removed from any catalytically active strands via cleavage of a ribonucleotide base. This allows the catalytic strands to be separated by a column that specifically binds the tag, since the non-active strands will remain bound to the column while the active strands (which no longer possess the tag) flow through. A common set-up for this is a biotin tag with a streptavidin affinity column. [25] [26] Gel electrophoresis based separation can also be used in which the change in molecular weight of strands upon the cleavage reaction is enough to cause a shift in the location of the reactive strands on the gel. [26] After the selection step, the reactive pool is amplified via polymerase chain reaction (PCR) to regenerate and amplify the reactive strands, and the process is repeated until a pool of sufficient reactivity is obtained. Multiple rounds of selection are required because some non-catalytic strands will inevitably make it through any single selection step. Usually 4–10 rounds are required for unambiguous catalytic activity, [8] though more rounds are often necessary for more stringent catalytic conditions. After a sufficient number of rounds, the final pool is sequenced and the individual strands are tested for their catalytic activity. [26] The dynamics of the pool can be described through mathematical modeling, [27] which shows how oligonucleotides undergo competitive binding with the targets and how the evolutionary outcome can be improved through fine tuning of parameters.

Deoxyribozymes obtained through in vitro selection will be optimized for the conditions during the selection, such as salt concentration, pH, and the presence of cofactors. Because of this, catalytic activity only in the presence of specific cofactors or other conditions can be achieved using positive selection steps, as well as negative selection steps against other undesired conditions.

in vitro evolution

A similar method of obtaining new deoxyribozymes is through in vitro evolution. Though this term is often used interchangeably with in vitro selection, in vitro evolution more appropriately refers to a slightly different procedure in which the initial oligonucleotide pool is genetically altered over subsequent rounds through genetic recombination or through point mutations. [25] [26] For point mutations, the pool can be amplified using error-prone PCR to produce many different strands of various random, single mutations. As with in vitro selection, the evolved strands with increased activity will tend to dominate the pool after multiple selection steps, and once a sufficient catalytic activity is reached, the pool can be sequenced to identify the most active strands.

The initial pool for in vitro evolution can be derived from a narrowed subset of sequence space, such as a certain round of an in vitro selection experiment, which is sometimes also called in vitro reselection. [26] The initial pool can also be derived from amplification of a single oligonucleotide strand. As an example of the latter, a recent study showed that a functional deoxyribozyme can be selected through in vitro evolution of a non-catalytic oligonucleotide precursor strand. An arbitrarily chosen DNA fragment derived from the mRNA transcript of bovine serum albumin was evolved through random point mutations over 25 rounds of selection. Through deep sequencing analysis of various pool generations, the evolution of the most catalytic deoxyribozyme strand could be tracked through each subsequent single mutation. [28] This first successful evolution of catalytic DNA from a non-catalytic precursor could provide support for the RNA World hypothesis. In another recent study, an RNA ligase ribozyme was converted into a deoxyribozyme through in vitro evolution of the inactive deoxyribo-analog of the ribozyme. The new RNA ligase deoxyribozyme contained just twelve point mutations, two of which had no effect on activity, and had a catalytic efficiency of approximately 1/10 of the original ribozyme, though the researches hypothesized that the activity could be further increased through further selection. [29] This first evidence for transfer of function between different nucleic acids could provide support for various pre-RNA World hypotheses.

"True" catalysis?

Because most deoxyribozymes suffer from product inhibition and thus exhibit single-turnover behavior, it is sometimes argued that deoxyribozymes do not exhibit "true" catalytic behavior since they cannot undergo multiple-turnover catalysis like most biological enzymes. However, the general definition of a catalyst requires only that the substance speeds up the rate of a chemical reaction without being consumed by the reaction (i.e. it is not permanently chemically altered and can be recycled). Thus, by this definition, single-turnover deoxyribozymes are indeed catalysts. [6] Furthermore, many endogenous enzymes (both proteins and ribozymes) also exhibit single-turnover behavior, [6] and so the exclusion of deoxyribozymes from the rank of "catalyst" simply because it does not feature multiple-turnover behavior seems unjustified.

Applications

Although RNA enzymes were discovered before DNA enzymes, the latter have some distinct advantages. DNA is more cost-effective, and DNA can be made with longer sequence length and can be made with higher purity in solid-phase synthesis. [30] Several studies have shown the usage of DNAzymes to inhibit influenza A and B virus replication in host cells. [31] [32] [33] [34] [35] [36] DNAzymes have also been shown to inhibit the replication of SARS coronavirus (SARS-CoV), [36] Respiratory syncytial virus (RSV), [36] human rhinovirus 14 [37] and HCV [38]

Drug clinical trials

Asthma is characterized by eosinophil-induced inflammation motivated by a type 2 helper T cell (Th2). By targeting the transcription factor, GATA3, of the Th2 pathway, with DNAzyme it may be possible to negate the inflammation. The safety and efficacy of SB010, a novel 10-23 DNAzyme was evaluated, and found to have the ability to cleave and inactivate GATA3 messenger RNA in phase IIa clinical trials. Treatment with SB010 significantly offset both late and early asthmatic responses after allergen aggravation in male patients with allergic asthma. [39] The transcription factor GATA-3 is also an interesting target, of the DNAzyme topical formulation SB012, for a novel therapeutic strategy in ulcerative colitis (UC). UC is an idiopathic inflammatory bowel diseases defined by chronically relapsing inflammations of the gastrointestinal tract, and characterized by a superficial, continuous mucosal inflammation, which predominantly affects the large intestine. Patients that do not effectively respond to current UC treatment strategies exhibit serious drawbacks one of which may lead to colorectal surgery, and can result in a severely compromised quality of life. Thus, patients with moderate or severe UC may significantly benefit from these new therapeutic alternatives, of which SB012 is in phase I clinical trials. [40] Atopic dermatitis (AD) is a chronic inflammatory skin disorder, in which patients suffer from eczema, often severe pruritus on the affected skin, as well as complications and secondary infections. AD surfaces from an upregulation of Th2-modified immune responses, therefore a novel AD approach using DNAzymes targeting GATA-3 is a plausible treatment option. The topical DNAzyme SB011 is currently in phase II clinical trials. [41] DNAzyme research for the treatment of cancer is also underway. The development of a 10-23 DNAzyme that can block the expression of IGF-I (Insulin-like growth factor I, a contributor to normal cell growth as well as tumorigenesis) by targeting its mRNA could be useful for blocking the secretion of IGF-I from prostate storm primary cells ultimately inhibiting prostate tumor development. Additionally, with this treatment it is expected that hepatic metastasis would also be inhibited, via the inhibition of IGF-I in the liver (the major source of serum IGF-I). [15]

Sensors

DNAzymes have found practical use in metal biosensors. [42] [43] A DNAzyme based biosensor for lead ion was used to detect lead ion in water in St. Paul Public Schools in Minnesota. [44] Furthermore, DNAzymes have been used in combination of aptamers and nucleic acid bioreceptors for the development of a multiplex bioassay. [45]

Asymmetric 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. [46] 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.

Bioconjugation with hGQ DNAzyme

The hemin/G-Quadruplex DNAzyme consists of G-Quadruplex forming DNA that can bind the co-factor hemin (a.k.a. Fe(III)Protoporphyrin IX), forming a complex that can perform certain oxidation reaction in the presence of hydrogen peroxide. [47] This DNAzyme can oxidize small molecules, such as dopamine and adenosine triphosphate, [48] but can also be used for the modification of peptides [49] and proteins [50] [51] by attaching small molecules.

Other uses

Other uses of DNA in chemistry are in DNA-templated synthesis, Enantioselective catalysis, [52] DNA nanowires and DNA computing. [53]

See also

Related Research Articles

<span class="mw-page-title-main">DNA</span> Molecule that carries genetic information

Deoxyribonucleic acid is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

<span class="mw-page-title-main">Primer (molecular biology)</span> Short strand of RNA or DNA that serves as a starting point for DNA synthesis

A primer is a short single-stranded nucleic acid used by all living organisms in the initiation of DNA synthesis. A synthetic primer may also be referred to as an oligo, short for oligonucleotide. DNA polymerase enzymes are only capable of adding nucleotides to the 3’-end of an existing nucleic acid, requiring a primer be bound to the template before DNA polymerase can begin a complementary strand. DNA polymerase adds nucleotides after binding to the RNA primer and synthesizes the whole strand. Later, the RNA strands must be removed accurately and replace them with DNA nucleotides forming a gap region known as a nick that is filled in using an enzyme called ligase. The removal process of the RNA primer requires several enzymes, such as Fen1, Lig1, and others that work in coordination with DNA polymerase, to ensure the removal of the RNA nucleotides and the addition of DNA nucleotides. Living organisms use solely RNA primers, while laboratory techniques in biochemistry and molecular biology that require in vitro DNA synthesis usually use DNA primers, since they are more temperature stable. Primers can be designed in laboratory for specific reactions such as polymerase chain reaction (PCR). When designing PCR primers, there are specific measures that must be taken into consideration, like the melting temperature of the primers and the annealing temperature of the reaction itself. Moreover, the DNA binding sequence of the primer in vitro has to be specifically chosen, which is done using a method called basic local alignment search tool (BLAST) that scans the DNA and finds specific and unique regions for the primer to bind.

<span class="mw-page-title-main">RNA world</span> Hypothetical stage in the early evolutionary history of life on Earth

The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage.

<span class="mw-page-title-main">Peptide nucleic acid</span> Biological molecule

Peptide nucleic acid (PNA) is an artificially synthesized polymer similar to DNA or RNA.

Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small fragments of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, molecular cloning and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression, or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.

<span class="mw-page-title-main">Ribozyme</span> Type of RNA molecules

Ribozymes are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material and a biological catalyst, and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems.

<span class="mw-page-title-main">Locked nucleic acid</span> Biological molecule

A locked nucleic acid (LNA), also known as bridged nucleic acid (BNA), and often referred to as inaccessible RNA, is a modified RNA nucleotide in which the ribose moiety is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes. This structure provides for increased stability against enzymatic degradation. LNA also offers improved specificity and affinity in base-pairing as a monomer or a constituent of an oligonucleotide. LNA nucleotides can be mixed with DNA or RNA residues in a oligonucleotide.

<span class="mw-page-title-main">Aptamer</span> Oligonucleotide or peptide molecules that bind specific targets

Aptamers are short sequences of artificial DNA, RNA, XNA, or peptide that bind a specific target molecule, or family of target molecules. They exhibit a range of affinities, with variable levels of off-target binding and are sometimes classified as chemical antibodies. Aptamers and antibodies can be used in many of the same applications, but the nucleic acid-based structure of aptamers, which are mostly oligonucleotides, is very different from the amino acid-based structure of antibodies, which are proteins. This difference can make aptamers a better choice than antibodies for some purposes.

<span class="mw-page-title-main">Rolling circle replication</span> DNA synthesis technique

Rolling circle replication (RCR) is a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids. Some eukaryotic viruses also replicate their DNA or RNA via the rolling circle mechanism.

Threose nucleic acid (TNA) is an artificial genetic polymer in which the natural five-carbon ribose sugar found in RNA has been replaced by an unnatural four-carbon threose sugar. Invented by Albert Eschenmoser as part of his quest to explore the chemical etiology of RNA, TNA has become an important synthetic genetic polymer (XNA) due to its ability to efficiently base pair with complementary sequences of DNA and RNA. The main difference between TNA and DNA/RNA is their backbones. DNA and RNA have their phosphate backbones attached to the 5' carbon of the deoxyribose or ribose sugar ring, respectively. TNA, on the other hand, has it's phosphate backbone directly attached to the 3' carbon in the ring, since it does not have a 5' carbon. This modified backbone makes TNA, unlike DNA and RNA, completely refractory to nuclease digestion, making it a promising nucleic acid analog for therapeutic and diagnostic applications.

<span class="mw-page-title-main">Systematic evolution of ligands by exponential enrichment</span> Technique for producing oligonucleotides that specifically bind to a target

Systematic evolution of ligands by exponential enrichment (SELEX), also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands. These single-stranded DNA or RNA are commonly referred to as aptamers. Although SELEX has emerged as the most commonly used name for the procedure, some researchers have referred to it as SAAB and CASTing SELEX was first introduced in 1990. In 2015, a special issue was published in the Journal of Molecular Evolution in the honor of quarter century of the discovery of SELEX.

<span class="mw-page-title-main">Hammerhead ribozyme</span>

The hammerhead ribozyme is an RNA motif that catalyzes reversible cleavage and ligation reactions at a specific site within an RNA molecule. It is one of several catalytic RNAs (ribozymes) known to occur in nature. It serves as a model system for research on the structure and properties of RNA, and is used for targeted RNA cleavage experiments, some with proposed therapeutic applications. Named for the resemblance of early secondary structure diagrams to a hammerhead shark, hammerhead ribozymes were originally discovered in two classes of plant virus-like RNAs: satellite RNAs and viroids. They are also known in some classes of retrotransposons, including the retrozymes. The hammerhead ribozyme motif has been ubiquitously reported in lineages across the tree of life.

<span class="mw-page-title-main">Hairpin ribozyme</span> Enzymatic section of RNA

The hairpin ribozyme is a small section of RNA that can act as a ribozyme. Like the hammerhead ribozyme it is found in RNA satellites of plant viruses. It was first identified in the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where it catalyzes self-cleavage and joining (ligation) reactions to process the products of rolling circle virus replication into linear and circular satellite RNA molecules. The hairpin ribozyme is similar to the hammerhead ribozyme in that it does not require a metal ion for the reaction.

<span class="mw-page-title-main">Leadzyme</span>

Leadzyme is a small ribozyme (catalytic RNA), which catalyzes the cleavage of a specific phosphodiester bond. It was discovered using an in-vitro evolution study where the researchers were selecting for RNAs that specifically cleaved themselves in the presence of lead. However, since then, it has been discovered in several natural systems. Leadzyme was found to be efficient and dynamic in the presence of micromolar concentrations of lead ions. Unlike in other small self-cleaving ribozymes, other divalent metal ions cannot replace Pb2+ in the leadzyme. Due to obligatory requirement for a lead, the ribozyme is called a metalloribozyme.

<span class="mw-page-title-main">VS ribozyme</span>

The Varkud satellite (VS) ribozyme is an RNA enzyme that carries out the cleavage of a phosphodiester bond.

<span class="mw-page-title-main">Hepatitis delta virus ribozyme</span>

The hepatitis delta virus (HDV) ribozyme is a non-coding RNA found in the hepatitis delta virus that is necessary for viral replication and is the only known human virus that utilizes ribozyme activity to infect its host. The ribozyme acts to process the RNA transcripts to unit lengths in a self-cleavage reaction during replication of the hepatitis delta virus, which is thought to propagate by a double rolling circle mechanism. The ribozyme is active in vivo in the absence of any protein factors and was the fastest known naturally occurring self-cleaving RNA at the time of its discovery.

<span class="mw-page-title-main">Ligase ribozyme</span>

The RNA Ligase ribozyme was the first of several types of synthetic ribozymes produced by in vitro evolution and selection techniques. They are an important class of ribozymes because they catalyze the assembly of RNA fragments into phosphodiester RNA polymers, a reaction required of all extant nucleic acid polymerases and thought to be required for any self-replicating molecule. Ideas that the origin of life may have involved the first self-replicating molecules being ribozymes are called RNA World hypotheses. Ligase ribozymes may have been part of such a pre-biotic RNA world.

<span class="mw-page-title-main">Xeno nucleic acid</span> Synthetic nucleic acid analogues

Xeno nucleic acids (XNA) are synthetic nucleic acid analogues that have a different backbone than the ribose and deoxyribose found in the nucleic acids of naturally occurring RNA and DNA.

<span class="mw-page-title-main">Hatchet ribozyme</span> Self-cleaving ribozyme

Background: The hatchet ribozyme is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. Hatchet ribozymes were discovered by a bioinformatics strategy as RNAs Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH.

Professor Alison Todd is holder of 18 patents, and a co-founder and chief scientific officer of SpeeDx. The company manufactures and sells tests for detecting infectious pathogens and identifying antibiotic resistance. The biomedical company, co-founded by Todd, develops diagnostic tools. Todd mentors younger scientists and entrepreneurs, as well as advocating for greater gender diversity in leaders in STEM. ‘Nearly 60 per cent of medical science and health graduates are women, but we hold only 20 per cent of senior leadership positions in the field’.

References

  1. 1 2 3 Breaker RR (May 1997). "DNA enzymes". Nature Biotechnology. 15 (5): 427–431. doi:10.1038/nbt0597-427. PMID   9131619. S2CID   1918660.
  2. ↑ Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (November 1982). "Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena". Cell. 31 (1): 147–157. doi:10.1016/0092-8674(82)90414-7. PMID   6297745. S2CID   14787080.
  3. ↑ Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (December 1983). "The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme". Cell. 35 (3 Pt 2): 849–857. doi:10.1016/0092-8674(83)90117-4. PMID   6197186. S2CID   39111511.
  4. ↑ Köhler T, Patsis PA, Hahn D, Ruland A, Naas C, Müller M, Thiele J (April 2020). "DNAzymes as Catalysts for l-Tyrosine and Amyloid β Oxidation". ACS Omega. 5 (13): 7059–7064. doi: 10.1021/acsomega.9b02645 . PMC   7143405 . PMID   32280846.
  5. ↑ Breaker RR, Joyce GF (September 2014). "The expanding view of RNA and DNA function". Chemistry & Biology. 21 (9): 1059–1065. doi:10.1016/j.chembiol.2014.07.008. PMC   4171699 . PMID   25237854.
  6. 1 2 3 4 5 6 Silverman SK (October 2004). "Deoxyribozymes: DNA catalysts for bioorganic chemistry". Organic & Biomolecular Chemistry. 2 (19): 2701–2706. CiteSeerX   10.1.1.626.8241 . doi:10.1039/B411910J. PMID   15455136.
  7. ↑ Ponce-Salvatierra A, Boccaletto P, Bujnicki JM (January 2021). "DNAmoreDB, a database of DNAzymes". Nucleic Acids Research. 49 (D1): D76–D81. doi:10.1093/nar/gkaa867. PMC   7778931 . PMID   33053178.
  8. 1 2 3 Silverman SK (2005). "In vitro selection, characterization, and application of deoxyribozymes that cleave RNA". Nucleic Acids Research. 33 (19): 6151–6163. doi:10.1093/nar/gki930. PMC   1283523 . PMID   16286368.
  9. 1 2 Breaker RR, Joyce GF (December 1994). "A DNA enzyme that cleaves RNA". Chemistry & Biology. 1 (4): 223–229. doi:10.1016/1074-5521(94)90014-0. PMID   9383394.
  10. ↑ Lan T, Furuya K, Lu Y (June 2010). "A highly selective lead sensor based on a classic lead DNAzyme". Chemical Communications. 46 (22): 3896–3898. doi:10.1039/B926910J. PMC   3071848 . PMID   20407665.
  11. ↑ Breaker RR, Joyce GF (October 1995). "A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity". Chemistry & Biology. 2 (10): 655–660. doi:10.1016/1074-5521(95)90028-4. hdl: 2060/19980216755 . PMID   9383471. S2CID   8546430.
  12. ↑ Faulhammer D, Famulok M (1996-12-01). "The Ca2+ Ion as a Cofactor for a Novel RNA-Cleaving Deoxyribozyme". Angewandte Chemie International Edition in English. 35 (23–24): 2837–2841. doi:10.1002/anie.199628371. ISSN   1521-3773.
  13. ↑ Santoro SW, Joyce GF (April 1997). "A general purpose RNA-cleaving DNA enzyme". Proceedings of the National Academy of Sciences of the United States of America. 94 (9): 4262–4266. Bibcode:1997PNAS...94.4262S. doi: 10.1073/pnas.94.9.4262 . PMC   20710 . PMID   9113977.
  14. ↑ Cruz RP, Withers JB, Li Y (January 2004). "Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme". Chemistry & Biology. 11 (1): 57–67. doi: 10.1016/j.chembiol.2003.12.012 . hdl: 11375/23673 . PMID   15112995.
  15. 1 2 Fokina AA, Meschaninova MI, Durfort T, Venyaminova AG, François JC (March 2012). "Targeting insulin-like growth factor I with 10-23 DNAzymes: 2'-O-methyl modifications in the catalytic core enhance mRNA cleavage". Biochemistry. 51 (11): 2181–2191. doi:10.1021/bi201532q. PMID   22352843.
  16. ↑ Montserrat Pagès A, Hertog M, Nicolaï B, Spasic D, Lammertyn J (2023-09-05). "Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme". International Journal of Molecular Sciences. 24 (18): 13686. doi: 10.3390/ijms241813686 . ISSN   1422-0067. PMC   10531344 .
  17. ↑ Li J, Lu Y (2000-10-01). "A Highly Sensitive and Selective Catalytic DNA Biosensor for Lead Ions". Journal of the American Chemical Society. 122 (42): 10466–10467. doi:10.1021/ja0021316. ISSN   0002-7863.
  18. ↑ Wu P, Hwang K, Lan T, Lu Y (April 2013). "A DNAzyme-gold nanoparticle probe for uranyl ion in living cells". Journal of the American Chemical Society. 135 (14): 5254–5257. doi:10.1021/ja400150v. PMC   3644223 . PMID   23531046.
  19. ↑ Torabi SF, Wu P, McGhee CE, Chen L, Hwang K, Zheng N, et al. (May 2015). "In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing". Proceedings of the National Academy of Sciences of the United States of America. 112 (19): 5903–5908. Bibcode:2015PNAS..112.5903T. doi: 10.1073/pnas.1420361112 . PMC   4434688 . PMID   25918425.
  20. ↑ Ponce-Salvatierra A, Wawrzyniak-Turek K, Steuerwald U, Höbartner C, Pena V (January 2016). "Crystal structure of a DNA catalyst". Nature. 529 (7585): 231–234. Bibcode:2016Natur.529..231P. doi:10.1038/nature16471. PMID   26735012. S2CID   4461523.
  21. ↑ Borman S. "After Two Decades Of Trying, Scientists Report First Crystal Structure Of A DNAzyme | January 11, 2016 Issue - Vol. 94 Issue 2 | Chemical & Engineering News". cen.acs.org. Retrieved 2017-02-04.
  22. ↑ Ven K, Safdar S, Dillen A, Lammertyn J, Spasic D (January 2019). "Re-engineering 10-23 core DNA- and MNAzymes for applications at standard room temperature". Analytical and Bioanalytical Chemistry. 411 (1): 205–215. doi:10.1007/s00216-018-1429-4. PMID   30341659. S2CID   53010843.
  23. ↑ Chinnapen DJ, Sen D (January 2004). "A deoxyribozyme that harnesses light to repair thymine dimers in DNA". Proceedings of the National Academy of Sciences of the United States of America. 101 (1): 65–69. doi:10.1073/pnas.0305943101. PMC   314139 . PMID   14691255.
  24. ↑ Chinnapen DJ, Sen D (January 2004). "A deoxyribozyme that harnesses light to repair thymine dimers in DNA". Proceedings of the National Academy of Sciences of the United States of America. 101 (1): 65–69. Bibcode:2004PNAS..101...65C. doi: 10.1073/pnas.0305943101 . PMC   314139 . PMID   14691255.
  25. 1 2 3 Joyce GF (2004). "Directed evolution of nucleic acid enzymes". Annual Review of Biochemistry. 73 (1): 791–836. doi:10.1146/annurev.biochem.73.011303.073717. PMID   15189159.
  26. 1 2 3 4 5 6 7 Silverman SK (August 2008). "Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects". Chemical Communications (30): 3467–3485. doi:10.1039/B807292M. PMID   18654692. S2CID   9824687.
  27. ↑ Spill F, Weinstein ZB, Irani Shemirani A, Ho N, Desai D, Zaman MH (October 2016). "Controlling uncertainty in aptamer selection". Proceedings of the National Academy of Sciences of the United States of America. 113 (43): 12076–12081. arXiv: 1612.08995 . Bibcode:2016PNAS..11312076S. doi: 10.1073/pnas.1605086113 . PMC   5087011 . PMID   27790993.
  28. ↑ Gysbers R, Tram K, Gu J, Li Y (June 2015). "Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence". Scientific Reports. 5: 11405. Bibcode:2015NatSR...511405G. doi:10.1038/srep11405. PMC   4473686 . PMID   26091540.
  29. ↑ Paul N, Springsteen G, Joyce GF (March 2006). "Conversion of a ribozyme to a deoxyribozyme through in vitro evolution". Chemistry & Biology. 13 (3): 329–338. doi: 10.1016/j.chembiol.2006.01.007 . PMID   16638538.
  30. ↑ Kumar B, Asha K, Chauhan SP (2013-10-07). "DNAzyme Mediated Post-transcriptional Gene Silencing: A Novel Therapeutic Approach".
  31. ↑ Kumar B, Khanna M, Kumar P, Sood V, Vyas R, Banerjea AC (May 2012). "Nucleic acid-mediated cleavage of M1 gene of influenza A virus is significantly augmented by antisense molecules targeted to hybridize close to the cleavage site". Molecular Biotechnology. 51 (1): 27–36. doi:10.1007/s12033-011-9437-z. PMID   21744034. S2CID   45686564.
  32. ↑ Kumar B, Rajput R, Pati DR, Khanna M (September 2015). "Potent Intracellular Knock-Down of Influenza A Virus M2 Gene Transcript by DNAzymes Considerably Reduces Viral Replication in Host Cells". Molecular Biotechnology. 57 (9): 836–845. doi:10.1007/s12033-015-9876-z. PMID   26021603. S2CID   23234776.
  33. ↑ Kumar B, Kumar P, Rajput R, Saxena L, Daga MK, Khanna M (October 2013). "Sequence-specific cleavage of BM2 gene transcript of influenza B virus by 10-23 catalytic motif containing DNA enzymes significantly inhibits viral RNA translation and replication". Nucleic Acid Therapeutics. 23 (5): 355–362. doi:10.1089/nat.2013.0432. PMID   23971908.
  34. ↑ Zhang Z, Zhang S, Wang S (February 2017). "DNAzymes Dz13 target the c-jun possess antiviral activity against influenza A viruses". Microbial Pathogenesis. 103: 155–161. doi:10.1016/j.micpath.2016.12.024. PMID   28039102.
  35. ↑ Kumar B, Asha K, Khanna M, Ronsard L, Meseko CA, Sanicas M (April 2018). "The emerging influenza virus threat: status and new prospects for its therapy and control". Archives of Virology. 163 (4): 831–844. doi:10.1007/s00705-018-3708-y. PMC   7087104 . PMID   29322273.
  36. 1 2 3 Asha K, Kumar P, Sanicas M, Meseko CA, Khanna M, Kumar B (December 2018). "Advancements in Nucleic Acid Based Therapeutics against Respiratory Viral Infections". Journal of Clinical Medicine. 8 (1): 6. doi: 10.3390/jcm8010006 . PMC   6351902 . PMID   30577479.
  37. ↑ Schubert S, Gül DC, Grunert HP, Zeichhardt H, Erdmann VA, Kurreck J (October 2003). "RNA cleaving '10-23' DNAzymes with enhanced stability and activity". Nucleic Acids Research. 31 (20): 5982–5992. doi:10.1093/nar/gkg791. PMC   219472 . PMID   14530446.
  38. ↑ Roy S, Gupta N, Subramanian N, Mondal T, Banerjea AC, Das S (July 2008). "Sequence-specific cleavage of hepatitis C virus RNA by DNAzymes: inhibition of viral RNA translation and replication". The Journal of General Virology. 89 (Pt 7): 1579–1586. doi: 10.1099/vir.0.83650-0 . PMID   18559927.
  39. ↑ Krug N, Hohlfeld JM, Kirsten AM, Kornmann O, Beeh KM, Kappeler D, et al. (May 2015). "Allergen-induced asthmatic responses modified by a GATA3-specific DNAzyme". The New England Journal of Medicine. 372 (21): 1987–1995. doi:10.1056/nejmoa1411776. hdl: 1854/LU-6862585 . PMID   25981191.
  40. ↑ "Efficacy, Pharmacokinetics, Tolerability, Safety of SB012 Intrarectally Applied in Active Ulcerative Colitis Patients (SECURE)". ClinicalTrials.gov. Retrieved May 27, 2016.
  41. ↑ "Efficacy, Safety, Tolerability, Pharmacokinetics and Pharmacodynamics Study of the Topical Formulation SB011 Applied to Lesional Skin in Patients With Atopic Eczema". ClinicalTrail.gov. Retrieved May 27, 2016.
  42. ↑ Liu J, Lu Y (2004). "Optimization of a Pb2+-Directed Gold Nanoparticle/DNAzyme Assembly and Its Application as a Colorimetric Biosensor for Pb2+". Chem. Mater. 16 (17): 3231–38. doi:10.1021/cm049453j.
  43. ↑ Wei H, Li B, Li J, Dong S, Wang E (March 2008). "DNAzyme-based colorimetric sensing of lead (Pb(2+)) using unmodified gold nanoparticle probes". Nanotechnology. 19 (9): 095501. Bibcode:2008Nanot..19i5501W. doi:10.1088/0957-4484/19/9/095501. PMID   21817668. S2CID   5201672.
  44. ↑ "Lead in Water: St. Paul Schools Delayed Fixes". ABC 6 NEWS. Retrieved 2017-02-04.
  45. ↑ Montserrat Pagès A, Safdar S, Ven K, Lammertyn J, Spasic D (August 2021). "DNA-only bioassay for simultaneous detection of proteins and nucleic acids". Analytical and Bioanalytical Chemistry. 413 (20): 4925–4937. doi:10.1007/s00216-021-03458-6. PMC   8238030 . PMID   34184101.
  46. ↑ Roelfes G, Feringa BL (May 2005). "DNA-based asymmetric catalysis" (PDF). Angewandte Chemie. 44 (21): 3230–3232. doi:10.1002/anie.200500298. PMID   15844122.
  47. ↑ Travascio P, Li Y, Sen D (September 1998). "DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex". Chemistry & Biology. 5 (9): 505–517. doi: 10.1016/s1074-5521(98)90006-0 . PMID   9751647.
  48. ↑ Golub E, Albada HB, Liao WC, Biniuri Y, Willner I (January 2016). "Nucleoapzymes: Hemin/G-Quadruplex DNAzyme-Aptamer Binding Site Conjugates with Superior Enzyme-like Catalytic Functions". Journal of the American Chemical Society. 138 (1): 164–172. doi:10.1021/jacs.5b09457. PMID   26652164.
  49. ↑ Wintermans S, Keijzer JF, Dros M, Zuilhof H, Albada B (2021-09-08). "Aptamer‐Assisted Bioconjugation of Tyrosine Derivatives with hemin/G‐quadruplex (hGQ) DNAzyme Nucleoapzyme Nanostructures". ChemCatChem. 13 (21): 4618–4624. doi:10.1002/cctc.202101070. hdl: 1887/3238907 . ISSN   1867-3880. S2CID   238732951.
  50. ↑ Keijzer JF, Albada B (October 2020). "Site-Specific and Trigger-Activated Modification of Proteins by Means of Catalytic Hemin/G-quadruplex DNAzyme Nanostructures". Bioconjugate Chemistry. 31 (10): 2283–2287. doi:10.1021/acs.bioconjchem.0c00422. PMC   7581286 . PMID   32909740.
  51. ↑ Xu L, Liu S, Yang T, Shen Y, Zhang Y, Huang L, et al. (2019). "DNAzyme Catalyzed Tyramide Depositing Reaction for In Situ Imaging of Protein Status on the Cell Surface". Theranostics. 9 (7): 1993–2002. doi:10.7150/thno.31943. PMC   6485291 . PMID   31037152.
  52. ↑ García-Fernández A, Roelfez G (2012). "Chapter 9. Enantioselective catalysis at the DNA Scaffold". In Sigel A, Sigel H, Sigel RK (eds.). Interplay between Metal Ions and Nucleic Acids. Metal Ions in Life Sciences. Vol. 10. Springer. pp. 249–268. doi:10.1007/978-94-007-2172-2_9. ISBN   978-94-007-2171-5. PMID   22210342.
  53. ↑ Ito Y, Fukusaki E (2004). "DNA as a 'Nanomaterial'" (PDF). Journal of Molecular Catalysis B: Enzymatic. 28 (4–6): 155–166. doi:10.1016/j.molcatb.2004.01.016. Archived from the original (PDF) on 2005-10-28.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.