Aptamer-DNAzyme hairpins for amplified biosensing

Study on sensing strategy and performance of a microfluidic chemiluminescence aptazyme sensor

Aptamers are analogous to antibodies in their range of target recognition. G-quadruplex DNAzymes exhibit peroxidase-like activity toward certain specific reactions. Despite aptazyme sensors, based on aptamer and DNAzyme conjugates, have the potential to replace many conventional immune-biosensors; the mechanism concerning high background interference has scarcely been discussed. In this work, by taking a couple of aptazyme sensors with oligonucleotide sequences of adenosine aptamer and CatG4 DNAzyme, the sensing strategy dealing with the thermodynamic equilibrium of the functional oligonucleotide distribution had been studied. Oligonucleotide arrangement and cation condition were found important in modulating the shifting between Watson-Crick duplex and Hoogsteen G-quadruplex, which ultimately influenced sample and background signals. Notably, benefit from the microfluidic chemiluminescence detection, the developed aptazyme sensor achieved an absolute detection limit of 12 pmol adenosine with just 2 μL of pretreated sample solution consumption and satisfactory selectivity. The results have implication for better design of aptazyme sensor in the future.

Recent Advances for the Detection of Ochratoxin A

Ochratoxin A (OTA) is one of the mycotoxins secreted by Aspersillus and Penicillium that can easily colonize various grains like coffee, peanut, rice, and maize. Since OTA is a chemically stable compound that can endure the physicochemical conditions of modern food processing, additional research efforts have been devoted to develop sensitive and cost-effective surveillance solutions. Although traditional chromatographic and immunoassays appear to be mature enough to attain sensitivity up to the regulation levels, alternative detection schemes are still being enthusiastically pursued in an attempt to meet the requirements of rapid and cost-effective detections. Herein, this review presents recent progresses in OTA detections with minimal instrumental usage, which have been facilitated by the development of OTA aptamers and by the innovations in functional nanomaterials. In addition to the introduction of aptamer-based OTA detection techniques, OTA-specific detection principles are also presented, which exclusively take advantage of the unique chemical structure and related physicochemical characteristics.

Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications

This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications of these systems. The assembly of computational modules composed of DNAzymes has led to the operation of a universal set of logic gates, to field programmable logic gates and computing circuits, to the development of multiplexers/demultiplexers, and to full-adder systems. Also, DNAzyme cascades operating as logic gates and computing circuits were demonstrated. DNAzyme logic systems find important practical applications. These include the use of DNAzyme-based systems for sensing and multiplexed analyses, for the development of controlled release and drug delivery systems, for regulating intracellular biosynthetic pathways, and for the programmed synthesis and operation of cascades.

Isothermal Amplification of Nucleic Acids

Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.

Adenosine Triphosphate-Triggered Release of Macromolecular and Nanoparticle Loads from Aptamer/DNA-Cross-Linked Microcapsules

The synthesis of stimuli-responsive DNA microcapsules acting as carriers for different payloads, and being dissociated through the formation of aptamer-ligand complexes is described. Specifically, stimuli-responsive anti-adenosine triphosphate (ATP) aptamer-cross-linked DNA-stabilized microcapsules loaded with tetramethylrhodamine-modified dextran (TMR-D), CdSe/ZnS quantum dots (QDs), or microperoxidase-11 (MP-11) are presented. In the presence of ATP as trigger, the microcapsules are dissociated through the formation of aptamer-ATP complexes, resulting in the release of the respective loads. Selective unlocking of the capsules is demonstrated, and CTP, GTP, or TTP do not unlock the pores. The ATP-triggered release of MP-11 from the microcapsules enables the MP-11-catalyzed oxidation of Amplex UltraRed by H2O2 to the fluorescent product resorufin.

DNAzyme-based biosensors and nanodevices

DNAzymes, screened through in vitro selection, have shown great promise as molecular tools in the design of biosensors and nanodevices. The catalytic activities of DNAzymes depend specifically on cofactors and show multiple enzymatic turnover properties, which make DNAzymes both versatile recognition elements and outstanding signal amplifiers. Combining nanomaterials with unique optical, magnetic and electronic properties, DNAzymes may yield novel fluorescent, colorimetric, surface-enhanced Raman scattering (SERS), electrochemical and chemiluminescent biosensors. Moreover, some DNAzymes have been utilized as functional components to perform arithmetic operations or as "walkers" to move along DNA tracks. DNAzymes can also function as promising therapeutics, when designed to complement target mRNAs or viral RNAs, and consequently lead to down-regulation of protein expression. This feature article focuses on the most significant achievements in using DNAzymes as recognition elements and signal amplifiers for biosensors, and highlights the applications of DNAzymes in logic gates, DNA walkers and nanotherapeutics.

Fluorometric detection of mutant DNA oligonucleotide based on toehold strand displacement-driving target recycling strategy and exonuclease III-assisted suppression

We describe here a fluorometric assay for sensitive detection of oligonucleotides, based on a target recycling amplification strategy driven by toehold-mediated strand displacement reaction and on exonuclease III (Exo Ш)-assisted fluorescence background suppression strategy. The network consists of a pair of partially complementary DNA hairpins (HP1 and HP2) with 3' overhang ends, between which the spontaneous hybridization is kinetically hindered by the stems. The target DNA is repeatedly used to trigger a recycling progress between the hairpins, generating numerous HP1-HP2 duplex complexes. Exo III was then employed to digest the double strand parts of the residual hairpins and the intermediate products. The fluorescent dye, SYBR Green I, binds to the double-strand DNA products and emits strong fluorescence to achieve sensitive detection of the target DNA with the detection limit of 5.34 pM. Moreover, this proposed strategy showed high discrimination efficiency towards target DNA against mismatched DNA and was successfully applied in the analysis of human serum sample.

A label-free activatable aptamer probe for colorimetric detection of cancer cells based on binding-triggered in situ catalysis of split DNAzyme

A novel label-free tailed hairpin-shaped activatable aptamer probe (THAAP) was developed by rationally integrating an aptamer and a split G-quadruplex into one sequence. Based on target recognition-triggered in situ catalysis of split DNAzyme, the THAAP strategy achieved a simple, fast, washing-free, specific and quantitative colorimetric assay of human leukemic CCRF-CEM cells.

Single-Molecule Visualization of the Activity of a Zn(2+)-Dependent DNAzyme

We demonstrate the single-molecule imaging of the catalytic reaction of a Zn(2+)-dependent DNAzyme in a DNA origami nanostructure. The single-molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high-speed atomic force microscopy (AFM). This nanostructure-based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single-molecule level.

A general approach to the design of allosteric, transcription factor-regulated DNAzymes

Here we explore a general strategy for the rational design of nucleic acid catalysts that can be allosterically activated by specific nucleic-acid binding proteins. To demonstrate this we have combined a catalytic DNAzyme sequence and the consensus sequence recognized by specific transcription factors to create a construct exhibiting two low-energy conformations: a more stable conformation lacking catalytic activity and lacking the transcription factor binding site, and a less stable conformation that is both catalytically active and competent to bind the transcription factor. The presence of the target transcription factor pushes the equilibrium between these states towards the latter conformation, concomitantly activating catalysis. To demonstrate this we have designed and characterized two peroxidase-like DNAzymes whose activities are triggered upon binding either TATA binding protein or the microphthalmia-associated transcription factor. Our approach augments the current tool kit for the allosteric control of DNAzymes and ribozymes and, because transcription factors control many key biological functions, could have important clinical and diagnostic applications.

A structure-switchable aptasensor for aflatoxin B1 detection based on assembly of an aptamer/split DNAzyme

An ultrasensitive, colorimetric and homogeneous strategy for aflatoxin B1 (AFB1) detection, which uses a DNA aptamer and two split DNAzyme halves, has been developed. Split halves of a hemin-binding DNAzymes is combined with an AFB1 aptamer to generate a homogeneous colorimetric sensor that undergoes an AFB1 induced DNA structural change. In the absence of AFB1, the split probes have peroxidase mimicking DNAzyme activity associated with catalysis of a color change reaction. Specific recognition of AFB1 by the aptamer component leads to structural deformation of the aptamer-DNAzyme complex, which causes splitting of the DNAzyme halves and a reduction in peroxidase mimicking activity. Therefore, a decrease of colorimetric signal arising from the catalytic process takes place upon in the presence of AFB1 in a concentration dependent manner in the 0.1-1.0 × 10(4) ng/mL range and with a colorimetric detection limit of 0.1 ng/mL. The new assay system exhibits high selectivity for AFB1 over other mycotoxins and can be employed detect the presence of AFB1 in ground corn samples. Overall, the strategy should serve as the basis for the development of rapid, simple and low-cost methods for detection of mycotoxins.

Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe

A series of luminescent iridium(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The iridium(iii) complex 9 [Ir(pbi)2(5,5-dmbpy)]PF6 (where pbi = 2-phenyl-1H-benzo[d]imidazole; 5,5-dmbpy = 5,5'-dimethyl-2,2'-bipyridine) exhibited high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a G-quadruplex-based assay for protein tyrosine kinase-7 (PTK7) in aqueous solution. PTK7 is an important biomarker for a range of leukemias and solid tumors. In the presence of PTK7, the specific binding of the sgc8 aptamer sequence triggers a structural transition and releases the G-quadruplex-forming sequence. The formation of the nascent G-quadruplex structure is then detected by the G-quadruplex-selective iridium(iii) complex with an enhanced luminescent response. Moreover, the application of the assay for detecting PTK7 in cellular debris and membrane protein extract was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for PTK7.

Studies on the effect of thymine-mercury-thymine stem as a structural or functional motif in DNAzymes

T-Hg-T base pair formation has been demonstrated to be compatible with duplex DNA context, with considerable thermal stability contribution. Here, the T-Hg-T stem in two small DNAzymes 8-17 and 10-23 was studied for its structural and functional roles. The recognition arm 5' to the cleavage site of 10-23 DNAzyme complex and the stem in the catalytic loop of 8-17 DNAzyme could be replaced by consecutive T-Hg-T stem of different length. The linear relationship between the activity of the complex 10-23DZ-6T+D19-6T and the concentration of Hg(2+) demonstrated that the T-Hg-T stem contributes thermal stability of the recognition arm binding. The effect of T-Hg-T stem in the catalytic core of 8-17 DNAzyme and the position-dependent effect in 10-23 DNAzyme demonstrated that T-Hg-T base pair is not compatible with canonical base pairs in playing the functions of nucleic acids.

Rationally designed molecular beacons for bioanalytical and biomedical applications

Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.

Steric-dependent label-free and washing-free enzyme amplified protein detection with dual-functional synthetic probes

Enzyme-catalyzed signal amplification with an antibody-enzyme conjugate is commonly employed in many bioanalytical methods to increase assay sensitivity. However, covalent labeling of the enzyme to the antibody, laborious operating procedures, and extensive washing steps are necessary for protein recognition and signal amplification. Herein, we describe a novel label-free and washing-free enzyme-amplified protein detection method by using dual-functional synthetic molecules to impose steric effects upon protein binding. In our approach, protein recognition and signal amplification are modulated by a simple dual-functional synthetic probe which consists of a protein ligand and an inhibitor. In the absence of the target protein, the inhibitor from the dual-functional probe would inhibit the enzyme activity. In contrast, binding of the target protein to the ligand perturbs this enzyme-inhibitor affinity due to the generation of steric effects caused by the close proximity between the target protein and the enzyme, thereby activating the enzyme to initiate signal amplification. With this strategy, the fluorescence signal can be amplified to as high as 70-fold. The generality and versatility of this strategy are demonstrated by the rapid, selective, and sensitive detection of four different proteins, avidin, O6-methylguanine DNA methyltransferase (MGMT), SNAP-tag, and lactoferrin, with four different probes.

Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems

This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.

Activation of Mg2+-dependent DNAzymes based on AP site-containing triplex for specific melamine recognition

A novel strategy for melamine recognition based on melamine binding-triggered triplex formation and DNAzyme activity regulation was developed.

Quartz crystal microbalance detection of protein amplified by nicked circling, rolling circle amplification and biocatalytic precipitation

A novel quartz crystal microbalance (QCM) assay was described for sensitive detection of protein. Lysozyme was used as a model of protein. To enhance the sensitivity of this QCM biosensor, biocatalytic precipitation (BCP) reaction combined with strand-scission cycle and rolling circle amplification (RCA) were applied together for the first time. As a result of the multi-signal amplification in this aptasensor, the detection limit for lysozyme was down to 0.3fM. What is more, this amplified QCM biosensor also showed good selectivity and practical usage in human serum.

Highly stable colorimetric aptamer sensors for detection of ochratoxin A through optimizing the sequence with the covalent conjugation of hemin

Optimization of hairpin DNA is introduced to detect ochratoxin A (OTA) by chemically conjugating its cofactor, hemin, toward the 5'-end. The newly designed OTA aptasensor showed enhanced stability and sensitivity, thereby lowering the detection limit to an ~1 nM level. Furthermore, an optimal spacer for hemin conjugation was investigated for stable responses toward very diluted OTA solutions.

N-Methyl-4-hydrazino-7-nitrobenzofurazan: a fluorogenic substrate for peroxidase-like DNAzyme, and its potential application

Characterization and optimization studies of N-methyl-4-hydrazino-7-nitrobenzofurazan (MNBDH) as a new fluorogenic substrate in the peroxidation reaction catalyzed by DNAzyme are reported. The effects of pH, H2O2 concentration, metal-cation type, and the concentration and type of surfactant on the fluorescence intensity were investigated. The optimized reaction was subsequently used for the development of an assay for DNA detection based on a molecular-beacon probe. The use of a fluorogenic substrate enabled the detection of a single-stranded DNA target with a 1 nmol L(-1) detection limit.

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 simple and highly sensitive DNAzyme-based assay for nicotinamide adenine dinucleotide by ligase-mediated inhibition of strand displacement amplification

Existing strategies for detecting nicotinamide adenine dinucleotide (NAD(+)) or other cofactors are commonly cumbersome and moderate sensitive. We report a novel DNAzyme-based visual assay strategy for NAD(+) based on ligase-mediated inhibition of the strand displacement amplification (SDA). In the presence of NAD(+), the SDA can be inhibited by the ligase reaction of two primers, which can initiate the SDA reaction in the case of no ligation, resulting in a dramatically decreasing yield of the SDA product, a G-quadruplex DNAzyme that can quantitatively catalyze the formation of a colored product. Therefore, the quantitative analysis for NAD(+) can be achieved visually with high sensitivity. The developed strategy provides a simple colorimetric approach with high selectivity against most interferences and a detection limit as low as 50 pM. It also provides a universal platform for investigating cofactors or other related small molecules as well as quantifying the activity of DNA ligases.

Signal propagation in multi-layer DNAzyme cascades using structured chimeric substrates

Signal propagation through enzyme cascades is a critical component of information processing in cellular systems. Although such systems have potential as biomolecular computing tools, rational design of synthetic protein networks remains infeasible. DNA strands with catalytic activity (DNAzymes) are an attractive alternative, enabling rational cascade design through predictable base-pair hybridization principles. Multi-layered DNAzyme signaling and logic cascades are now reported. Signaling between DNAzymes was achieved using a structured chimeric substrate (SCS) that releases a downstream activator after cleavage by an upstream DNAzyme. The SCS can be activated by various upstream DNAzymes, can be coupled to DNA strand-displacement devices, and is highly resistant to interference from background DNA. This work enables the rational design of synthetic DNAzyme regulatory networks, with potential applications in biomolecular computing, biodetection, and autonomous theranostics.

A novel electrochemical aptasensor for highly sensitive detection of thrombin based on the autonomous assembly of hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme nanowires

In this work, a new signal amplified strategy was constructed based on isothermal exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR) generating the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (HRP-mimicking DNAzyme) nanowires as signal output component for the sensitive detection of thrombin (TB). We employed EXPAR's ultra-high amplification efficiency to produce a large amount of two hairpin helper DNAs within a minutes. And then the resultant two hairpin helper DNAs could autonomously assemble the hemin/G-quadruplex HRP-mimicking DNAzymes nanowires as the redox-active reporter units on the electrode surface via hybridization chain reaction (HCR). The hemin/G-quadruplex structures simultaneously served as electron transfer medium and electrocatalyst to amplify the signal in the presence of H2O2. Specifically, only when the EXPAR reaction process has occurred, the HCR could be achieved and the hemin/G-quadruplex complexes could be formed on the surface of an electrode to give a detectable signal. The proposed strategy combines the amplification power of the EXPAR, HCR, and the inherent high sensitivity of the electrochemical detection. With such design, the proposed assay showed a good linear relationship within the range of 0.1 pM-50 nM with a detection limit of 33 fM (defined as S/N=3) for TB.

Optical aptasensors for quantitative detection of small biomolecules: a review

Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.

A theophylline quartz crystal microbalance biosensor based on recognition of RNA aptamer and amplification of signal

A quartz crystal microbalance (QCM) biosensor for theophylline was developed by recognition of RNA aptamer and gold nanoparticle amplification technique. Firstly, a designed small single-stranded RNA, RNA1, was immobilized onto the QCM electrode through a thiol linker. Then, the complementary stranded RNA2, which can combine with RNA1 to form a double-stranded RNA with a recognition unit of theophylline, could be self-assembled on the QCM electrode surface through a hybrid reaction in the presence of theophylline. The recognition process could cause a frequency change of QCM to give the signal related to theophylline. When RNA2 was tethered to gold nanoparticles, the signal could be amplified to further enhance the sensitivity of the designed sensor. Under the optimal conditions, the QCM-based biosensor showed excellent sensitivity (limit of detection, 8.2 nM) and specificity with a dissociation constant of Kd = 5.26 × 10(-7) M. The sensor can be used to quantitatively detect theophylline in serum, suggesting that it can be applied in complex biological samples.

Homogeneous assay of target molecules based on chemiluminescence resonance energy transfer (CRET) using DNAzyme-linked aptamers

We have designed a single-stranded DNAzyme-aptamer sensor for homogeneous target molecular detection based on chemiluminescence resonance energy transfer (CRET). The structure of the engineered single-stranded DNA (ssDNA) includes the horseradish peroxidase (HRP)-like DNAzyme, optimum-length linker (10-mer-length DNA), and target-specific aptamer sequences. A quencher dye was modified at the 3' end of the aptamer sequence. The incorporation of hemin into the G-quadruplex structure of DNAzyme yields an active HRP-like activity that catalyzes luminol to generate a chemiluminescence (CL) signal. In the presence of target molecules, such as ochratoxin A (OTA), adenosine triphosphate (ATP), or thrombin, the aptamer sequence was folded due to the formation of the aptamer/analyte complex, which induced the quencher dye close to the DNAzyme structure. Consequently, the CRET occurred between a DNAzyme-catalyzed chemiluminescence reaction and the quencher dye. Our results showed that CRET-based DNAzyme-aptamer biosensing enabled specific OTA analysis with a limit of detection of 0.27ng/mL. The CRET platform needs no external light source and avoids autofluorescence and photobleaching, and target molecules can be detected specifically and sensitively in a homogeneous manner.

A simple label-free electrochemical aptasensor for dopamine detection

A simple and label-free electrochemical biosensor based on a dopamine DNA aptamer was developed for the sensitive and selective detection of dopamine.

A new colorimetric strategy for monitoring caspase 3 activity by HRP-mimicking DNAzyme–peptide conjugates

A new colorimetric method is designed for the detection of caspase 3 activity by HRP-mimicking DNAzyme–peptide conjugates.

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.

Novel homogeneous label-free electrochemical aptasensor based on functional DNA hairpin for target detection

We first developed a label-free and immobilization-free homogeneous electrochemical aptasensor, which combined a smart functional DNA hairpin and a designed miniaturized electrochemical device. Cocaine was chosen as a model target. The anticocaine aptamer and peroxidase-mimicking DNAzyme were integrated into one single-stranded DNA hairpin. Both aptamer and G-quadruplex were elaborately blocked by the stem region. The conformation switching induced by the affinity interaction between aptamer and cocaine released G-quadruplex part and turned on DNAzyme activity. The designed electrochemical device, constructed by a disposable micropipet tip and a reproducible carbon fiber ultramicroelectrode, was applied to the detection of homogeneous DNAzyme catalytic activity at the microliter level. The aptasensor realized the quantification of cocaine ranging from 1 to 500 μM with high specificity. The clever combination of the functional DNA hairpin and the novel device achieved an absolutely label-free electrochemical aptasensor, which showed excellent performance like low cost, easy operation, rapid detection, and high repeatability.

Allosterically tunable, DNA-based switches triggered by heavy metals

Here we demonstrate the rational design of allosterically controllable, metal-ion-triggered molecular switches. Specifically, we designed DNA sequences that adopt two low energy conformations, one of which does not bind to the target ion and the other of which contains mismatch sites serving as specific recognition elements for mercury(II) or silver(I) ions. Both switches contain multiple metal binding sites and thus exhibit homotropic allosteric (cooperative) responses. As heterotropic allosteric effectors we employ single-stranded DNA sequences that either stabilize or destabilize the nonbinding state, enabling dynamic range tuning over several orders of magnitude. The ability to rationally introduce these effects into target-responsive switches could be of value in improving the functionality of DNA-based nanomachines.

Proximity-dependent protein detection based on enzyme-assisted fluorescence signal amplification

In this paper, we develop a sensitive fluorescence method for protein detection based on proximity extension and enzyme-assisted signal amplification. In this novel method, pairs of proximity probes are designed, and the recognition elements are integrated into the proximity probes. Then proteins are detected by transforming aptamer or antibody-protein binding signals into DNA detection based on proximity effect. In addition, nick sites are introduced into the proximity probes to amplify the detectable signal. As proof of concept, detection of human α-thrombin and human IgG are demonstrated in this study. The aptamers and antibodies are coupled in the proximity probes as recognition elements for human α-thrombin and human IgG respectively. In the presence of target protein, aptamer or antibody-protein binding signals are transformed into detectable signals by the proximity effect, and can be further amplified by enzyme-assisted strand displacement. The above mentioned strategies consequently bring the limit of detection (LOD) to as low as 1 pM for human α-thrombin and 6 pM for human IgG. Furthermore, this method might be extended to sensitive detection of other proteins by changing recognition elements of proximity probes.

Protein-binding aptamer assisted signal amplification for the detection of influenza A (H1N1) DNA sequences based on quantum dot fluorescence polarization analysis

We report a fluorescence polarization platform for H1N1 detection based on the construction of a DNA functional QD fluorescence polarization probe and a bi-functional protein binding aptamer (Apt-DNA). The assay has a linear range from 10 nM to 100 nM with a detection limit of 3.45 nM and is selective over the mismatched bases.

Label-free electrochemiluminescent detection of DNA by hybridization with a molecular beacon to form hemin/G-quadruplex architecture for signal inhibition

A facile label-free electrochemiluminescent (ECL) DNA sensor was designed using a molecular beacon with a guanine-rich stem as a recognition probe. The ECL emission was produced from surface unpassivated CdTe quantum dots (QDs) co-immobilized with colloidal gold nanoparticles (AuNPs) on a chitosan-modified electrode surface. The molecular beacon was adsorbed onto the AuNPs by the thiolated stem. Upon the hybridization of the molecular beacon with target DNA to open the cycle in the presence of hemin, the dissociated guanine-rich sequence could conjugate hemin to form a G-quadruplex architecture. The formed DNAzyme then catalyzed the reduction of dissolved oxygen, the endogenous coreactant for ECL emission of QDs, leading to a decrease in ECL signal. The variations in surface morphology during the fabrication and recognition processes of the ECL sensor were characterized by atomic force microscopy and electrochemical impedance spectroscopy. The ECL signal inhibition depended linearly on the logarithmic value of DNA concentration ranging from 5.0 fM to 0.1 nM, with a detection limit of 0.9 fM. This proposed label-free method is a promising application of QDs-based ECL emission for ultrasensitive DNA assay.

A novel electrochemical aptasensor for thrombin detection based on the hybridization chain reaction with hemin/G-quadruplex DNAzyme-signal amplification

In this work, a novel signal amplification electrochemical aptasensor for the sensitive and selective detection of thrombin was successfully fabricated. The amplification method was based on the hybridization chain reaction (HCR) and a pseudobienzyme electrocatalytic system. HCR-based double-stranded DNA (dsDNA) polymers not only constructed an effective carrier for anchoring larger amounts of electron mediator methylene blue (MB) into the DNA duplexes to produce a strong differential pulse voltammetry (DPV) signal, but also resulted in the formation of hemin/G-quadruplex DNAzymes nanowires by intercalating hemin into two induced single-stranded DNA (ssDNA). With the addition of NADH into the electrolytic cell, the hemin/G-quadruplex acting as an NADH oxidase and HRP-mimicking DNAzyme for the pseudobienzyme amplifying system could in situ biocatalyze the formation of H₂O₂ with local concentrations and low transfer loss resulting in dramatic signal enhancements. The binding event can be detected by a decrease in the integrated charge of MB which electrostatically absorbed onto dsDNA polymers. In the presence of thrombin, the dsDNA polymers associated with MB and hemin/G-quadruplex structures were removed from the electrode surface, leading to a significant decrease of redox current. DPV signals of MB provided quantitative measures of the concentrations of thrombin, with a linear calibration range of 0.01-50 nM and a detection limit of 2 pM. Moreover, the resulting aptasensor also exhibited good specificity, acceptable reproducibility and stability, indicating that the present strategy was promising for broad potential application in clinic assay and various protein analyses.