A DNA oligonucleotide-hemin complex cleaves t-butyl hydroperoxide through a homolytic mechanism

Visual Assay for Methicillin-Resistant Staphylococcus aureus Based on Rolling Circular Amplification Triggering G-Quadruplex/Hemin DNAzyme Proximity Assembly

Nowadays, infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have constituted a new challenge for anti-infective treatment. Precise identification and rapid clinical diagnostics of MRSA from other methicillin-sensitive strains entail assays with robust diagnostic efficiency and simple operation steps. Sensitive detection of MecA gene is promising to indicate MRSA infection, but it is challenged by the lack of isothermal and simple strategies. A visual assay based on isothermal rolling circular amplification and G-quadruplex/hemin (G4/hemin) DNAzyme proximity assembly was proposed for the immediate, efficient, and cost-effective detection of MecA in simple operation steps and in a single tube. The presence of MecA specifically drove the formation of circular templates, which further triggered isothermal amplification. The amplified product offered abundant binding sites for DNA-grafted hemin probes to form a novel proximity-assembled G4/hemin DNAzyme structure for colorimetric changing diagnosis. This tandem-repeated novel DNAzyme possessed higher catalytic activity and a lower background signal than traditional G4/hemin DNAzyme, ensuring sensitive discrimination of MRSA (limit of detection: 9.6 pM). Assay stability and antimatrix interference capability enable clinical application, which shows compared diagnostic ability with classic methods (100% sensitivity and 100% specificity) but possesses more simplified procedures and shorter turnaround time (<6 h). This colorimetric strategy in a nonsite-specific and hypersensitive manner holds foreseeable prospects in clinical diagnostic and research applications.

In vivo self-degradable graphene nanomedicine operated by DNAzyme and photo-switch for controlled anticancer therapy

Although graphene oxide (GO) possesses many beneficial functionalities for biomedical usage as itself, modification of GO surface with several polymers or protein is inevitable for in vivo applications; however, such modification limits the degradability of GO due to the steric hindrance. In that context, designing of a surface modified GO carrier that is going to be degraded after its biological function (i.e., drug delivery) is highly desired, especially at complex in vivo level. Herein, we design an unprecedented "catalytic GO nanomedicine" by applying the catalytic DNA, achieving self-degradation of GO in systemic level in the body after the therapy following surface modification. Once the catalytic GO nanomedicines are taken up by mucin1 (MUC1) aptamer-facilitated endocytosis, a photo-switch triggers the release of doxorubicin from the DNA. The single stranded G-quadruplex sequence on the surface of GO forms a quartet structure and becomes DNAzyme by binding with hemin on the GO surface, exhibiting peroxidase effect. Due to the high H₂O₂ concentration in cancer cells, the catalytic GO nanomedicine generates sufficient amount of strong oxidant, hypochlorous acid (HOCl), inducing GO degradation into small fragments for potential clearance. We demonstrate the potential of our catalytic GO nanomedicine for both therapy and degradation at cellular and complex in vivo environment.

Toward a Rational Approach to Design Split G-Quadruplex Probes

Hybridization probes have become an indispensable tool for nucleic acid analysis. Systematic efforts in probe optimization resulted in their improved binding affinity, turn-on ratios, and ability to discriminate single nucleotide substitutions (SNSs). The use of split (or multicomponent) probes is a promising strategy to improve probe selectivity and enable an analysis of folded analytes. Here, we developed criteria for the rational design of a split G-quadruplex (G4) peroxidase-like deoxyribozyme (sPDz) probe that provides a visual output signal. The sPDz probe consists of two DNA strands that hybridize to the abutting positions of a DNA/RNA target and form a G4 structure catalyzing, in the presence of a hemin cofactor, H₂O₂-mediated oxidation of organic compounds into their colored oxidation products. We have demonstrated that probe design becomes complicated in the case of target sequences containing clusters (two or more) of cytosine residues and developed strategies to overcome the challenges to achieving high signal-to-noise and excellent SNS discrimination. Specifically, to improve selectivity, a conformational constraint that stabilizes the probe's dissociated state is beneficial. If the signal intensity is compromised, introduction of flexible non-nucleotide linkers between the G4-forming and target-recognizing elements of the probe helps to decrease the steric hindrance for G4 PDz formation observed as a signal increase. Varying the modes of G4 core splitting is another instrument for the optimal sPDz design. The suggested algorithm was successfully utilized for the design of the sPDz probe interrogating a fragment of the Influenza A virus genome (subtype H1N1), which can be of practical use for flu diagnostics and surveillance.

Characterization of the interaction between heme and a parallel G-quadruplex DNA formed from d(TTGAGG)

Structure-function relationships of complexes between heme and G-quadruplex DNAs have attracted interest from researchers in related fields. A carbon monoxide adduct of a complex between heme and a parallel G-quadruplex DNA formed from hexanucleotide d(TTGAGG) (heme-[d(TTGAGG)]₄ complex) has been characterized using ¹H NMR spectroscopy, and the obtained results were compared with those for the heme-[d(TTAGGG)]₄ complex previously studied in order to elucidate the effect of the incorporation of an A-quartet into stacked G-quartets in the 3'-terminal region of the DNA on the structure of the heme-DNA complex. We found that a π-π stacking interaction between the porphyrin moiety of the heme and the 3'-terminal G-quartet of the DNA is affected by the nature of the stacked G-quartets. This finding provides novel insights as to the design of the molecular architecture of a heme-DNA complex. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

DNA sensors and aptasensors based on the hemin/G-quadruplex-controlled aggregation of Au NPs in the presence of L-cysteine

L-cysteine induces the aggregation of Au nanoparticles (NPs), resulting in a color transition from red to blue due to interparticle plasmonic coupling in the aggregated structure. The hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme catalyzes the aerobic oxidation of L-cysteine to cystine, a process that inhibits the aggregation of the NPs. The degree of inhibition of the aggregation process is controlled by the concentration of the DNAzyme in the system. These functions are implemented to develop sensing platforms for the detection of a target DNA, for the analysis of aptamer-substrate complexes, and for the analysis of L-cysteine in human urine samples. A hairpin DNA structure that includes a recognition site for the DNA analyte and a caged G-quadruplex sequence, is opened in the presence of the target DNA. The resulting self-assembled hemin/G-quadruplex acts as catalyst that controls the aggregation of the Au NPs. Also, the thrombin-binding aptamer folds into a G-quadruplex nanostructure upon binding to thrombin. The association of hemin to the resulting G-quadruplex aptamer-thrombin complex leads to a catalytic label that controls the L-cysteine-mediated aggregation of the Au NPs. The hemin/G-qaudruplex-controlled aggregation of Au NPs process is further implemented for visual and spectroscopic detection of L-cysteine concentration in urine samples.

A novel electrochemical DNA biosensor based on HRP-mimicking hemin/G-quadruplex wrapped GOx nanocomposites as tag for detection of Escherichia coli O157:H7

A novel sensitive electrochemical DNA biosensor was developed for amperometric detection of Escherichia coli O157:H7 (E. coli O157:H7). The graphene oxide (GOx) was utilized as nanocarrier to immobilize thionine (Thi) and the Au nanoparticles coated SiO2 nanocomposites (Au-SiO2) by electrostatic adsorption and the adsorption among nanomaterials. Then a large amounts of signal DNA (S2) and G-quadruplex were immobilized on the GOx-Thi-Au@SiO2 nanocomposites. Finally, hemin was intercalated into the G-quadruplex to obtain the hemin/G-quadruplex structure as HRP-mimicking DNAzyme. On the basis of the signal amplification strategy of GOx-Thi-Au@SiO2 nanocomposites and DNAzyme, the developed DNA biosensor could respond to 0.01 nM (S/N=3) with a linear calibration range from 0.02 to 50.0 nM E. coli O157:H7, which could be well accepted for early clinical detection. The studied system provides new opportunities, and might speed up disease diagnosis, treatment and prevention with pathogen.

Selenite-mediated production of superoxide radical anions in A549 cancer cells is accompanied by a selective increase in SOD1 concentration, enhanced apoptosis and Se-Cu bonding

Selenite may exert its cytotoxic effects against cancer cells via the generation of reactive oxygen species (ROS). We investigated sources of, and the cellular response to, superoxide radical anion (O2 (·-)) generated in human A549 lung cancer cells after treatment with selenite. A temporal delay was observed between selenite treatment and increases in O2 (·-) production and biomarkers of apoptosis/necrosis, indicating that the reduction of selenite by the glutathione reductase/NADPH system (yielding O2 (·-)) is a minor contributor to ROS production under these conditions. By contrast, mitochondrial and NADPH oxidase O2 (·-) generation were the major contributors. Treatment with a ROS scavenger [poly(ethylene glycol)-conjugated superoxide dismutase (SOD) or sodium 4,5-dihydroxybenzene-1,3-disulfonate] 20 h after the initial selenite treatment inhibited both ROS generation and apoptosis determined at 24 h. In addition, SOD1 was selectively upregulated and its perinuclear cytoplasmic distribution was colocalised with the cellular distribution of selenium. Interestingly, messenger RNA for manganese superoxide dismutase, catalase, inducible haem oxygenase 1 and glutathione peroxidase either remained unchanged or showed a delayed response to selenite treatment. Colocalisation of Cu and Se in these cells (Weekley et al. in J. Am. Chem. Soc. 133:18272-18279, 2011) potentially results from the formation of a Cu-Se species, as indicated by Cu K-edge extended X-ray absorption fine structure spectra. Overall, SOD1 is upregulated in response to selenite-mediated ROS generation, and this likely leads to an accumulation of toxic hydrogen peroxide that is temporally related to decreased cancer cell viability. Increased expression of SOD1 gene/protein coupled with formation of a Cu-Se species may explain the colocalisation of Cu and Se observed in these cells.

Hemin/G-quadruplex-catalyzed aerobic oxidation of thiols to disulfides: application of the process for the development of sensors and aptasensors and for probing acetylcholine esterase activity

This study describes the novel hemin/G-quadruplex DNAzyme-catalyzed aerobic oxidation of thiols to disulfides and the respective mechanism. The mechanism of the reaction involves the DNAzyme-catalyzed oxidation of thiols to disulfides and the thiol-mediated autocatalytic generation of H2O2 from oxygen. The coupling of a concomitant H2O2-mediated hemin/G-quadruplex-catalyzed oxidation of Amplex Red to the fluorescent resorufin as a transduction module provides a fluorescent signal for probing the catalyzed oxidation of the thiol to disulfides and for probing sensing processes that yield the hemin/G-quadruplex as a functional label. Accordingly, a versatile sensing method for analyzing thiols (L-cysteine, glutathione) using the H2O2-mediated DNAzyme-catalyzed oxidation of Amplex Red to the resorufin was developed. Also, the L-cysteine and Amplex Red system was implemented as an auxiliary fluorescent transduction module for probing recognition events that form the catalytic hemin/G-quadruplex structures. This is exemplified with the development of thrombin aptasensor. The thrombin/thrombin binding aptamer recognition complex binds hemin, and the resulting catalytic complex activates the auxiliary transduction module, involving the aerobic oxidation of l-cysteine and the concomitant formation of the fluorescent resorufin. Finally, the hemin/G-quadruplex DNAzyme/Amplex Red system was used to follow the activity of acetylcholine esterase, AChE, and to probe its inhibition. The AChE-catalyzed hydrolysis of acetylthiocholine to the thiol-functionalized thiocholine enabled the probing of the enzymatic activity of AChE through the hemin/G-quadruplex-catalyzed aerobic oxidation of thiocholine to the respective disulfide and the concomitant generation of the fluorescent resorufin product.

Nucleic acid/quantum dots (QDs) hybrid systems for optical and photoelectrochemical sensing

Nucleic acid/semiconductor quantum dots (QDs) hybrid systems combine the recognition and catalytic properties of nucleic acids with the unique photophysical features of QDs. These functions of nucleic acid/QDs hybrids are implemented to develop different optical sensing platforms for the detection of DNA, aptamer-substrate complexes, and metal ions. Different photophysical mechanisms including fluorescence, electron transfer quenching, fluorescence resonance energy transfer (FRET), and chemiluminescence resonance energy transfer (CRET) are used to develop the sensor systems. The size-controlled luminescence properties of QDs are further implemented for the multiplexed, parallel analysis of several DNAs, aptamer-substrate complexes, or mixtures of ions. Similarly, methods to amplify the sensing events through the biocatalytic regeneration of the analyte were developed. An additional paradigm in the implementation of nucleic acid/QDs hybrids for sensing applications involves the integration of the systems with electrodes, and the generation of photocurrents as transduction signals for the sensing events. Finally, semiconductor QDs conjugated to functional DNA machines, such as "walker" systems, provide an effective optical label for probing the dynamics and mechanical functions of the molecular devices. The present article addresses the recent advances in the application of nucleic acid/QDs hybrids for sensing applications and DNA nanotechnology, and discusses future perspectives of these hybrid materials.

DNA-decorated nanoparticles as nanosensors for rapid detection of ascorbic acid

We designed an assay for rapid detection of ascorbic acid (AA) with a DNAzyme cleaving its DNA substrate in the presence of Cu(2+) and AA. The sensor consists of two DNA strands that form a complex between each other. The 5'-end of the DNAzyme binds the substrate DNA via Watson-Crick bonding and the 3'-end binds through formation of a DNA-triplex via Hoogsteen hydrogen bonding. The substrate DNA was prepared by two different methods. In the first case the nucleic acid was modified with fluorescein/dabcyl FRET pair across the cleavage site. In the second case the nucleic acid modified with fluorescein was immobilised on gold nanoparticles. DNAzyme contains a loop forming a complex with Cu(2+) ions. The oxidation of ascorbic acid (AA) with oxygen yields hydrogen peroxide. The latter interacts with Cu(2+) to give hydroxyl radicals. They break substrate DNA in close vicinity to the copper/DNA complex to separate fluorescein from gold nanoparticles leading to the increase in fluorescence intensity. Use of substrate DNA modified with the fluorescein/dabcyl couple allowed to measure AA concentration within 3 min with the detection limit of 2.5 μM. Employment of gold nanoparticles decorated with fluorescein-modified DNA allowed to improve the detection limit of AA quantification by two orders of magnitude due to enhanced cleavage of DNA catalysed by Au clusters. Fructose, sucrose, glucose, urea, and citric acid did not interfere with our assay even at concentration of 1mM. Good selectivity allowed us to apply our rapid and sensitive assays to detection of AA in vitamin C tablets, urine and orange juice.

RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean?

Guanine-rich RNAs and DNAs from chromosomal telomeres and elsewhere that fold into guanine quadruplexes (G-quadruplexes), are found to complex tightly with porphyrins such as N-methylmesoporphyrin IX (NMM) and hemin [Fe(III) heme]. By themselves, these DNAs and RNAs are found to be efficient catalysts for porphyrin metallation. When complexed with hemin, under physiological conditions, these nucleic acids display robust peroxidase (one-electron oxidation), as well as peroxygenase (two-electron oxidation, or oxygen transfer) activity. These surprising catalytic properties, that frequently match the catalytic performance of natural peroxidase and P450 monooxygenase enzymes, have been the subject of significant mechanistic analysis, as well as having found utility in a wide range of biosensing and other applications. This review summarizes recent insights into a surprising yet fundamental property of many RNAs and DNAs, a property with undoubted ramifications for cellular oxidative disease, de novo hemoenzyme design, and our understanding of the evolution of early biocatalytic systems.

Hemin/G-quadruplexes as DNAzymes for the fluorescent detection of DNA, aptamer-thrombin complexes, and probing the activity of glucose oxidase

Hemin/G-quadruplex catalyzes the H(2)O(2)-mediated oxidation of Amplex Red to the fluorescent product resorufin. This process is implemented to develop hairpin nucleic acid structures for the detection of DNA, to probe the catalytic activity of glucose oxidase, to use the thrombin-aptamer complex as a catalytic readout structure, and to quantitatively analyze telomere chain composition.

DNA-based peroxidation catalyst--what is the exact role of topology on catalysis and is there a special binding site for catalysis?

In the last decade, there has been growing interests in studies aimed at delineating the strategies used by various nucleic acid enzymes to facilitate catalysis. Insights gained from such studies would enable the design of better DNA/RNA catalysts for various applications such as biosensing. DNA and RNA catalysts have been shown to be able to catalyze myriads of reactions, including peroxidation reactions, which are catalyzed by G-quadruplexes. In this report, we provide data that clarifies how G-quadruplex peroxidases achieve catalysis. Firstly, we show that by covalently linking a hemin cofactor to DNAzymes, anti-parallel G-quadruplexes, which have been previously shown to be catalytically inefficient, can be "resurrected" to become good peroxidation catalysts. We also reveal that the relative rates of peroxidation by DNAzyme peroxidases depend on the nature of the organic reductant, arguing for a special binding site in the peroxidase-mimicking DNAzymes for catalysis.

Tuning of peroxidase activity by covalently tethered DNA oligonucleotides

We report on the modulation of the peroxidase activity of hybrid catalysts, comprising short DNA oligonucleotides and heme enzymes by means of sequence variation of tethered oligonucleotides. In particular, binary mixtures of native heme (protophorphyrin IX) and single-stranded DNA oligonucleotides as well as the analogous covalent heme-oligonucleotide conjugates were compared with DNA-enzyme conjugates, prepared by reconstitution of apo-myoglobin or apo-horseradisch peroxidase, using the aforementioned covalent heme-oligonucleotide conjugates. In all systems, it was clearly evident that the implemented oligonucleotides markedly influence the catalytic activity in a sequence-dependent matter. Greater than 100-fold changes in catalytic constants were observed, depending on which oligonucleotide was incorporated in the hybrid catalyst. We also observed that the tethered oligomers affect the inhibition of HRP-mediated peroxidation by means of small molecule inhibitors. On the basis of the quantitative description of this phenomenon and consideration of the current state of knowledge, we hypothesize that distinct interactions, such as hydrogen bonding or electrostatic contacts, occur between the oligonucleotides and the heme-containing catalyst, which account for the effects observed.

Rational design of an optical adenosine sensor by conjugating a DNA aptamer with split DNAzyme halves

Split halves of a hemin-binding DNAzyme have been assembled with an anti-adenosine aptamer to build a homogeneous allosteric sensor for adenosine with high selectivity and sensitivity.

Catalytic DNAzymes: derivations and functions

BACKGROUND

Although catalytic RNA enzymes (CRzs) are naturally occurring in many organisms, their DNA counterparts (CDzs) were developed by in vitro selection/evolution from random sequence libraries.

OBJECTIVE

To provide a brief overview of how CDzs have been selected in vitro, and of their properties and functions, as well as their possible future utility.

METHODS

We concentrated on examples of 'direct' selection of CDzs. Many CDzs have been used in biological settings, for example downregulation of target mRNAs, while many more recent applications use CDzs in biosensor and nanotechnology settings.

CONCLUSIONS

Although much work has concentrated on using CDzs for regulating gene expression, their potential as nucleic acid medicines has diminished substantially, supplanted by simple antisense oligonucleotides and, more recently, by small interfering RNAs (siRNAs). It seems unlikely that CDzs will have clinical utility. In contrast, they are likely to have significant potential in the sensor/nanotechnology arena.

The reaction of artemisinins with hemoglobin: A unified picture

The reactions with hemoglobin of artemisinin and of its parent compounds, sodium artesunate and dihydroartemisinin, were investigated by visible absorption spectroscopy under standard solution conditions (50 mM phosphate buffer, pH 7, 37 degrees C). Notably, these antimalarial drugs were found to react with hemoglobin (i.e., ferrous heme), but not with methemoglobin (i.e., ferric heme). The reaction selectively occurs at the heme sites and consists of the progressive, slow decay of the Soret band, as a consequence of heme alkylation and subsequent loss of pi electron delocalization. For the various tested compounds the process reaches completion within approximately 30-70 h. Additional experiments were carried out upon adopting the solution conditions described by Meunier et al. and by Kannan et al. in their recent studies. Some reactivity of artemisinin with methemoglobin was indeed detected after addition of 50% v/v acetonitrile, most likely as a consequence of extensive protein unfolding. A unified description for the reactions of artemisinins with hemoglobin is given.

Amplified chemiluminescence surface detection of DNA and telomerase activity using catalytic nucleic acid labels

A G-rich nucleic acid sequence binds hemin and yields a biocatalytic complex (DNAzyme) of peroxidase activity, namely, the biocatalyzed generation of chemiluminescence in the presence of H(2)O(2) and luminol. The DNAzyme is used as a label for the amplified detection of DNA, or for the analysis of telomerase activity in cancer cells, using chemiluminescence as an output signal. In one configuration, the analyzed DNA is hybridized with a primer nucleic acid that is associated with a Au surface, and the DNAzyme label is hybridized with the surface-confined analyte DNA. The DNA is analyzed with a detection limit of approximately 1 x 10(-)(9) M. In the second system, telomerase from HeLa cancer cells induces telomerization of a primer associated with a Au surface and the complementary DNAzyme units are hybridized with the telomere to yield the chemiluminescence. The detection limit of the system corresponds to 1000 HeLa cells in the analyzed sample.

Spectrophotometric and ESI-MS/HPLC studies reveal a common mechanism for the reaction of various artemisinin analogues with hemin

The reaction of hemin with three well known artemisinin analogues, namely dihydroartemisinin, artemether and artesunate, was independently analysed by visible spectrophotometry and by ESI-MS/HPLC. A very similar reaction pathway emerges for all these compounds that matches closely the reaction profile previously described for artemisinin. In the course of the reaction characteristic isomeric 1:1 drug-hemin adducts are formed as in the case of artemisinin; eventual disruption of the porphyrin ring takes place in all cases, most likely through oxidative degradation.

Stoichiometric and catalytic activation of the alpha- and beta-2,3,4-tri-O-acetyl-5-thioxylopyranosyl bromide inside the cavity of the Pd3(dppm)3(CO)2+ cluster

The title cluster (Pd(3)(2+)) exhibits a pronounced affinity for Br(-) ions to form the very stable Pd(3)(Br)(+) adduct. Upon a 2-electron reduction, a dissociative process occurs generating Pd(3)(0) and eliminating Br(-) according to an ECE mechanism (electrochemical, chemical, electrochemical). At a lower temperature (i.e. -20 degrees C), both ECE and EEC processes operate. This cluster also activates the C-Br bond, and this work deals with the reactivity of Pd(3)(2+) with 2,3,4-tri-O-acetyl-5-thioxylopyranosyl bromide (Xyl-Br), both alpha- and beta-isomers. The observed inorganic product is Pd(3)(Br)(+) again, and it is formed according to an associative mechanism involving Pd(3)(2+).Xyl-Br host-guest assemblies. In an attempt to render the C-Br bond activation catalytic, these species are investigated under reduction conditions at two potentials (-0.9 and -1.25 V vs SCE). In the former case, the major product is Xyl-H, issued from a radical intermediate Xyl(*) abstracting an H atom from the solvent. Evidence for Xyl(*) is provided by the trapping with TEMPO (2,2,6,6-tetramethyl-1-piperidinyloxy) and DMPO (5,5'-dimethylpyrroline-N-oxyde). In the second case, only one product is observed, 3,4-di-O-acetyl-5-thioxylal, which is issued from the Xyl(-)() intermediate anion.