G-quadruplex-based DNAzyme for facile colorimetric detection of thrombin

Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates

As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.

An off-on fluorescence aptasensor for trace thrombin detection based on FRET between CdS QDs and AuNPs

An off-on fluorescence aptasensor was developed for trace thrombin detection based on fluorescence resonance energy transfer (FRET) between CdS QDs and gold nanoparticles (AuNPs). Using DNA pairwise hybridization of the aptamer to the complementary DNA (cDNA), the CdS QDs (energy donor) were tightly coupled to the AuNPs (energy acceptor), resulting in the occurrence of FRET and there was a dramatic fluorescence quenching of CdS QDs (turn off). When the thrombin was added to the fluorescence aptasensor, the specific binding of the aptamer to the target formed a G-quadruplex that caused the AuNPs receptor to detach and the DNA duplex to be disassembled. The process would inhibit the FRET which contribute to the recovery of fluorescence (turn on) and an "off-on" fluorescence aptasensor for thrombin detection was constructed accordingly. Under optimal conditions, the fluorescence recovery showed good linearity with the concentration of thrombin in the range of 1.35-54.0 nmol L-1, and the detection limit was 0.38 nmol L-1 (S/N = 3, n = 9). Importantly, the fluorescence aptasensor presented excellent specificity for thrombin, and was successfully applied to the quantitative determination of thrombin in real serum with satisfactory recoveries of 98.60-102.2%.

Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes

The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na⁺, K⁺, Ag⁺, Tl⁺, Cu⁺/Cu²⁺, Hg²⁺, and Pb²⁺) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.

Luminescent Aptamer-Based Bioassays for Sensitive Detection of Food Allergens

The presence of hidden allergens in food products, often due to unintended contamination along the food supply chain (production, transformation, processing, and transport), has raised the urgent need for rapid and reliable analytical methods for detecting trace levels of such species in food products. Indeed, food allergens represent a high-risk factor for allergic subjects due to potentially life-threatening adverse reactions. Portable biosensors based on immunoassays have already been developed as rapid, sensitive, selective, and low-cost analytical platforms that can replace analyses with traditional bench-top instrumentation. Recently, aptamers have attracted great interest as alternative biorecognition molecules for bioassays, since they can bind a variety of targets with high specificity and selectivity, and they enable the development of assays exploiting a variety of transduction and detection technologies. In particular, aptasensors based on luminescence detection have been proposed, taking advantage of the development of ultrasensitive tracers and enhancers. This review aims to summarize and discuss recent efforts in the field of food allergen analysis using aptamer-based bioassays with luminescence detection.

The Recent Progress in DNAzymes-Based Aptasensors for Thrombin Detection

Thrombin (TB) is classified among human blood coagulation proteins with key functions in hemostasis of blood vessels, wound healing, atherosclerosis, tissue adhesion, etc. Moreover, TB is involved as the main enzyme in the conversion of the fibrinogen to fibrin. Given the importance of TB detection in the clinical area, the development of innovative methods can considerably improve TB detection. Newly, aptasensors or aptamer-based biosensors have received special attention for sensitive and facile TB detection. In addition, the aptamer/nanomaterial conjugates have presented new prospects in accurate TB detection as nanoaptasensors. DNA-based enzymes or DNAzymes, as new biocatalysts, have many advantages over protein enzymes and can be used in analytical tools. This article reviews a brief overview of significant progresses regarding the various types of DNAzymes-based aptasensors and nano aptasensors developed for thrombin detection. In the following, challenges and prospects of TB detection by DNAzymes-based aptasensors are discussed.

Aptamer-Based Sensors for Thrombin Detection Application

Thrombin facilitates the aggregation of platelet in hemostatic processes and participates in the regulation of cell signaling. Therefore, the development of thrombin sensors is conducive to comprehending the role of thrombin in the course of a disease. Biosensors based on aptamers screened by SELEX have exhibited superiority for thrombin detection. In this review, we summarized the aptamer-based sensors for thrombin detection which rely on the specific recognitions between thrombin and aptamer. Meanwhile, the unique advantages of different sensors including optical and electrochemical sensors were also highlighted. Especially, these sensors based on electrochemistry have the potential to be miniaturized, and thus have gained comprehensive attention. Furthermore, concerns about aptamer-based sensors for thrombin detection, prospects of the future and promising avenues in this field were also presented.

Regulation of the Structure of Zirconium-Based Porphyrinic Metal-Organic Framework as Highly Electrochemiluminescence Sensing Platform for Thrombin

An electrochemiluminescence (ECL) sensor provides a sensitive and convenient method for early diagnosis of diseases; however, it is still a challenge to develop simple and sensitive sensing platforms based on efficient ECL signals and luminophore groups. Porphyrin-based metal-organic frameworks (MOFs) show great potential in ECL sensing; however, the mechanism and structure-activity relationship, as well as application, are rarely reported. Herein, hydrothermal reactions obtained porphyrin Zr-MOFs (PCN-222) with different specific surface areas, pore sizes, structures, and surface charge states by tuning the reaction time were developed, which served both as the ECL luminophore, coreaction promoter for S₂O₈^2-, and a connection in the ECL immunoassay. By progressively controlling the condition of the hydrothermal reaction, PCN-222 with large surface area-abundant micropores can be obtained, which has good conductivity and positively charged surfaces, obtaining excellent ECL performance. The ECL performance and the enhancement mechanism were investigated in detail. Using PCN-222-6h with the best ECL intensity as the immobilization matrix for the aptamer, a highly sensitive and selective assay for thrombin was developed. The decrease of the ECL signal was logarithmically linear with the concentration of thrombin in the range from 50 fg mL^-1 to 100 pg mL^-1 with a low detection limit of 2.48 fg/mL. This proposed strategy provides a brand new approach for tuning of the structures of MOFs as effective ECL signal probes, thus providing wider possibilities for effective ECL immunoassays in the detection of other biomarkers in diagnosis of diseases.

Manipulating the Assembly of DNA Nanostructures and Their Enzymatic Properties by Incorporating a 5'-5' Polarity of Inversion Site in the G-Tract

Supramolecular DNA complexes consisting of both DNA duplexes and tetrameric G-quadruplexes are fabricated successfully by utilizing a single short DNA strand that contains one 5'-5' polarity of inversion site in the middle of G-tract. The resulting DNA supramolecules exhibit significantly high peroxidase activities after interaction with hemin due to the presence of various G-quadruplex-duplex (G4-duplex) interfaces. Significantly, we find that the addition of a C-rich fragment to the designed sequence not only allows the self-assembly of two-dimensional porous DNA nanostructures via the formation of dimeric i-motif structures but also could act as a control element to facilitate the generation of pH-sensitive G4-based DNAzymes. The enhanced catalytic activity obtained from specific sequence modifications as well as the controllable feature of these DNA nanostructures can significantly benefit further applications of DNA functional materials in complex biological systems.

Competitive aptasensor with gold nanoparticle dimers and magnetite nanoparticles for SERS-based determination of thrombin

It is known that the intensity of surface-enhanced Raman scattering (SERS) of monomeric gold nanoparticles (GNPs) is insufficient for ultrasensitive analysis. The authors describe dimeric GNPs for use in a competitive SERS and aptamer based assay for thrombin. The reagent 1,2-bis(4-pyridyl) ethylene serves as both the coupling agent and the Raman reporter on the GNP dimers. In the presence of thrombin, the hybridization of two aptamers, one attached to the GNP dimers, the other to magnetic nanoparticles, is competitively prevented. This method takes advantage of the unique "hot spots" of the GNP dimers to amplify the Raman signal. This results in an ultra-sensitive thrombin assay when compared to assays using GNP monomers. The limit of detection is as low as 1 fM of thrombin. The Raman intensity, best measured at 1612 cm^-1, increases linearly in the 1 fM to 10 nM thrombin concentration range. The method was applied to the determinaiton of thrombin in spiked simulated body fluid and human serum. Graphical abstract This method takes advantage of the unique "hot spots" of the gold nanoparticle dimers to amplify the Raman signal. The dimers are linked to the magnetic nanoparticles via an aptamer. The use of both competitive displacement and magnetic separation greatly improves the sensitivity of the thrombin assay.

Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges

DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.

Dual Aptamer-Functionalized 3D Plasmonic Metamolecule for Thrombin Sensing

DNA nanotechnology offers the possibility to rationally design structures with emergent properties by precisely controlling their geometry and functionality. Here, we demonstrate a DNA-based plasmonic metamolecule that is capable of sensing human thrombin proteins. The chiral reconfigurability of a DNA origami structure carrying two gold nanorods was used to provide optical read-out of thrombin binding through changes in the displayed plasmonic circular dichroism. In our experiments, each arm of the structure was modified with one of two different thrombin-binding aptamers—thrombin-binding aptamer (TBA) and HD22—in such a way that a thrombin molecule could be sandwiched by the aptamers to lock the metamolecule in a state of defined chirality. Our structure exhibited a Kd of 1.4 nM, which was an order of magnitude lower than those of the individual aptamers. The increased sensitivity arose from the avidity gained by the cooperative binding of the two aptamers, which was also reflected by a Hill coefficient of 1.3 ± 0.3. As we further exploited the strong plasmonic circular dichroism (CD) signals of the metamolecule, our method allowed one-step, high sensitivity optical detection of human thrombin proteins in solution.

A Label-free Resonance Rayleigh Scattering Sensor for Detection of Thrombin Based on Aptamer Recognizing

The interaction between thrombin binding aptamer (TBA) and thrombin (TB) was studied by resonance Rayleigh scattering (RRS). In neutral medium, TBA is present in a balanced form between a G-quadruplex structure and a random coil structure, and the TBA can be induced by metal ions to form a G-quadruplex structure. Upon addition of thrombin, the G-quadruplex selectively bound to TB, which resulted in enhanced resonance Rayleigh scattering. The scattering intensities increased proportionally with the concentration of TB from 10 to 50 nM. The method had very high sensitivity and good selectivity, and the detection limit (3δ/s) was 1 nM. In this work, the spectral characteristics of RRS, the optimum conditions of the reaction, and influencing factors for the RRS intensities were investigated. Furthermore, the structure of the TBA-TB complex and the sensing mechanism were explored. The TB sensor was applied to a diluted human serum sample with satisfactory results, indicating the potential of this method to be applied to biological samples. A selective and simple RRS sensor for the detection of trace amounts of TB is proposed based on conformational change of TBA.

A colorimetric aptamer biosensor based on cationic polythiophene derivative as peroxidase mimetics for the ultrasensitive detection of thrombin

A colorimetric assay for the ultrasensitive determination of thrombin was presented, in which the cationic polythiophene derivative was used as catalyst of the 3,3',5,5'-tetramethylbenzidine (TMB)-H₂O₂ reaction and the thrombin-binding aptamer (TBA) was used as inducing polymer's different conformation elements. It was found the cationic polythiophene derivative, poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-t-hiophene hydrochloride] (PMNT), can catalyze the oxidation reaction of TMB in the presence of H₂O₂ to produce a blue color solution. The catalytic activity of PMNT on the TMB-H₂O₂ reaction was closely relevant to the conformation of PMNT. The absorbance of TMB-H₂O₂ was distinctly increased in the presence of TBA. With the addition of thrombin, TBA interacted with thrombin to form a G-quadruplex structure. The conformational change weakened the catalytic activity of PMNT and resulted in a decrease in the absorbance. The colorimetric sensor could detect thrombin down to 4pM with high selectivity against other interfering proteins. This work is not only of importance for a better understanding of the unique properties of cationic polythiophenes derivative but also have great potential for medical diagnostics and therapy for human health.

Highly sensitive electrochemical thrombin aptasensor based on peptide-enhanced electrocatalysis of hemin/G-quadruplex and nanocomposite as nanocarrier

In this work, we first conjugated a short peptide to thrombin binding aptamer (TBA) and bond hemin to the hybrid, effectively rendering hemin/G4-peptide more active over the original hemin/G4, so that a highly sensitive electrochemical thrombin (TB) aptasensor was developed based on it and PtNTs@rGO nanocomposite. It was the first report on the application of hemin/G4-peptide in electrochemical aptasensor. PtNTs@rGO with large surface area served as excellent nanocarrier for high loading of hemin/G4-peptide hybrids, resulting in the formation of hemin/G4-peptide-PtNTs@rGO bioconjugate as the secondary aptamer and further signal enhancement. The specific affinity of aptamer for target TB made the secondary aptamer go into the sensing interface, and then a noticeable current signal was obtained from hemin without additional redox mediators. Due to the collaborative electrocatalysis of hemin/G4-peptide and PtNTs toward H₂O₂, which was formed in situ during the process of hemin/G4-peptide-catalyzed oxidation of NADH with dissolved O₂, the current intensity increased dramatically. Such an electrochemical aptasensing system could be used to detect TB with a linear range of 0.05 pM-60nM and very lower detection limit of 15fM. Notably, this method exhibited a higher sensitivity than that of many hemin/G4-based electrochemical strategies for TB detection due to the improvement of the catalytic activity of hemin/G4-peptide. The present works opened a new way for expanding the application of hemin/G4 in biological detection. With the mediator-free, proteinous enzyme-free yet high-sensitivity advantages, this electrochemical aptasensor held great promise for other biomarker detections in clinical diagnostics.

G-quadruplex-based aptamers against protein targets in therapy and diagnostics

Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

Silver Nanoclusters Beacon as Stimuli-Responsive Versatile Platform for Multiplex DNAs Detection and Aptamer-Substrate Complexes Sensing

An activatable silver nanoclusters beacon (ASNCB) was synthesized through a facile one-pot approach and applied for multiplex DNAs, small molecule, and protein sensing. Multifunctional single-stranded DNA sequences are rationally designed and used for ASNCB in situ synthesis. Via target-responsive structure transformation of ASNCB, target recognition induced ASNCB conformational transition and lit up the fluorescent signal of silver nanoclusters. By further implementing two different color ASNCBs (520 and 600 nm), the parallel multiplexed analysis of two target genes (Influenza A virus genes H1N1 and H5N1) is achieved. Additionally, with the introduction of aptamer for the design of the molecular beacon, the detections of small molecule adenosine triphosphate (ATP) and biomacromolecule thrombin have also been realized. This is the first time that an activatable fluorescent silver nanoclusters (Ag NCs)-based probe and the target recognition have been integrated into a single process, which provides a versatile platform for different analytes in a facile way. The successful application of our proposed ASNCB in real sample analysis and ATP imaging in living cells further displayed its promising potential for fluorescence sensing.

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.

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.

Microfluidic chip-based silver nanoparticles aptasensor for colorimetric detection of thrombin

In this paper, a colorimetric silver nanoparticles aptasensor (aptamer-AgNPs) was developed for simple and straightforward detection of protein in microfluidic chip. Surface-functionalized microfluidic channels were employed as the capture platform. Then the mixture of target protein and aptamer-AgNPs were injected into the microfluidic channels for colorimetric detection. To demonstrate the performance of this detection platform, thrombin was chosen as a model target protein. Introduction of thrombin could form a sandwich-type complex involving immobilized AgNPs. The amount of aptamer-AgNPs on the complex augmented along with the increase of the thrombin concentration causing different color change that can be analyzed both by naked eyes and a flatbed scanner. This method is featured with low sample consumption, simple processes of microfluidic platform and straightforward colorimetric detection with aptamer-AgNPs. Thrombin at concentrations as low as 20pM can be detected using this aptasensor without signal amplification. This work demonstrated that it had good selectivity over other proteins and it could be a useful strategy to detect other targets with two affinity binding sites for ligands as well.

Stability and bioactivity of thrombin binding aptamers modified with D-/L-isothymidine in the loop regions

Thrombin binding aptamer (TBA) is a 15-mer single-strand DNA that was identified by SELEX screening technology. It adopts a chair-type antiparallel G-quadruplex and can specifically interact with thrombin, thus inhibiting blood coagulation. Isonucleoside (isoNA) is a type of nucleoside isomer in which the base is shifted to 2′-positions of the glycosyl group, endowed with the ability to modulate local conformation of nucleotides, and L-isoNA could alter the conformation more due to the inversion of glycosyl configuration. Incorporation of L-isothymidine (L-isoT) at T3, T9, T12 positions and D-isoT at the T7 position in TBA's loop regions promoted the formation of G-quadruplex, resulting in enhanced affinity with thrombin and an increased anticoagulant effect. Computer simulation indicated that TBA-12L showed the strongest binding with thrombin, which was consistent with experimental results. The bioactivity of double isoNA incorporated TBA with D-IsoT at T7 and L-IsoT at T12 was comparable to that of TBA-12L, suggesting that the T12 of TBA was very important in interaction with thrombin. Our study also suggested that TBA might interact with two thrombin molecules through the TT loops (T3T4, T12T13) and TGT loop, but the second bonding did not show additional biological effects.

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.

Metalloporphyrin/G-quadruplexes: From basic properties to practical applications

Guanine-rich single-stranded nucleic acids self-assemble into G-quadruplex nanostructures (predominately in the presence of K +-ions). Metalloporphyrins bind to the G-quadruplex nanostructures to form supramolecular assemblies exhibiting unique catalytic, electrocatalytic and photophysical properties. This paper addresses the advances in the characterization and the implementation of the metalloporphyrin/G-quadruplexes complexes for various applications. Out of the different complexes, the most extensively studied complexes are the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme and the Zn(II) -protoporphyrin IX-functionalized G-quadruplex. Specifically, the hemin/G-quadruplex was found to act as a catalyst for driving different chemical transformations that mimic the native horseradish peroxidase enzyme, and, also, to function as an electrocatalyst for the reduction of H 2 O 2. Also, the hemin/G-quadruplex stimulates interesting photophysical and photocatalytic processes such as the electron-transfer quenching of semiconductor quantum dots or the chemiluminescence resonance energy transfer to semiconductor quantum dots. Alternatively, Zn(II) -protoporphyrin IX associated with G-quadruplexes exhibit intensified fluorescence properties. Beyond the straight forward application of the metalloporphyrin/G-quadruplexes as catalysts that stimulate different chemical transformations, the specific catalytic, electrocatalytic and photocatalytic functions of hemin/G-quadruplexes are heavily implemented to develop sophisticated colorimetric, electrochemical, and optical sensing platforms. Also, the unique fluorescence properties of Zn(II) -protoporphyrin IX-functionalized G-quadruplexes are applied to develop fluorescence sensing platforms. The article exemplifies different sensing assays for analyzing DNA, ligand-aptamer complexes and telomerase activity using the metalloporphyrins/G-quadruplexes as transducing labels. Also, the use of the hemin/G-quadruplex as a probe to follow the operations of DNA machines is discussed.

Up-conversion fluorescence "off-on" switch based on heterogeneous core-satellite assembly for thrombin detection

NaGdF4: Yb, Er nanoparticles, with up-conversion (UC) fluorescence, were used for the first time to build an "off-on" switch based on Au core-UC satellites for thrombin detection. We fabricated the fluorescence sensor using thrombin aptamer modified Au core and complementary sequence modified UC satellites in liquid phase. With optimized assembled conditions, the yield of Au core-UC satellites achieved 80%. The fluorescence of UC nanoparticles quenched when satellite NP attached to Au core NP. Thrombin aptamer on the surface of Au core would bind to targets when thrombin existed in the system, then UC satellites were released and the quenched fluorescence recovered. The sensor showed high specificity for thrombin compared with other biomolecules and the limit of detection reached 3.5 fg/mL. Application of this sensor to detect targets in human serum also achieved satisfactory results. The purpose of this work was to build an ultrasensitive sensor based on Au core-UC satellites for thrombin detection in human serum to achieve diagnosis of diseases.

Photocatalytic oxidation of TMB with the double stranded DNA–SYBR Green I complex for label-free and universal colorimetric bioassay

The previously undiscovered photocatalytic activity of the classical dsDNA–SYBR Green complex for TMB oxidation was reported here for label-free and universal visual bioassays.

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.

Synthetic multivalent DNAzymes for enhanced hydrogen peroxide catalysis and sensitive colorimetric glucose detection

A peroxidase-mimic DNAzyme is a G-quadruplex (G4) DNA-hemin complex, in which the G4-DNA resembles an apoenzyme, and hemin is the cofactor for hydrogen peroxide (H2O2) catalysis. Twenty-one-mer CatG4 is a well-proven G4-DNA as well as a hemin-binding aptamer for constituting a DNAzyme. This work studied if a multivalent DNAzyme with accelerated catalysis could be constructed using a multimeric CatG4 with hemin. We compared CatG4 monomer, dimer, trimer, and tetramer, which were prepared by custom oligo synthesis, for G4 structure formation. According to circular dichroism (CD) analysis, we found that a CatG4 multimer exhibited more active G4 conformation than the sum effect of equal-number CatG4 monomers. However, the DNAzyme kinetics was not improved monotonically along with the subunit number of a multimeric CatG4. It was the trivalent DNAzyme, trimeric CatG4:hemin, resulting in the rapidest H2O2 catalysis instead of a tetravalent one. We discovered that the trivalent DNAzyme's highest catalytic rate was correlated to its most stable hemin-binding G4 structure, evidenced by CD melting temperature analysis. Finally, a trivalent DNAzyme-based colorimetric glucose assay with a detection limit as low as 10 μM was demonstrated, and this assay did not need adenosine 5'-tri-phosphate disodium salt hydrate (ATP) as a DNAzyme boosting agent.

Binding-induced and label-free colorimetric method for protein detection based on autonomous assembly of hemin/G-quadruplex DNAzyme amplification strategy

In this work, a new binding-induced and label-free colorimetric method for protein detection has been developed on the basis of an autonomous assembly of hemin/G-quadruplex DNAzyme amplification strategy. The system consists of two proximity probes carrying two aptamer sequences as recognition elements for target, and two hairpin structures include three-fourths and one-fourth of the G-quadruplex sequences in inactive configuration as functional elements. In the presence of target protein, two proximity probes bind to the protein simultaneously, forming a stable DNA-protein complex. Then the complex triggers an autonomous cross-opening of the two functional hairpin structures, leading to the formation of numerous hemin/G-quadruplex DNAzymes. The resulting DNAzymes catalyze the oxidation of colorless 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(2-)) to the green-colored ABTS(•-) with the presence of H2O2, thus providing the amplified colorimetric detection of target. Using human α-thrombin as the protein target, this binding-induced DNAzyme amplification colorimetric method affords high sensitivity with a detection limit of 1.9 pM. Furthermore, this method might be further extended to sensitive detection of other proteins by simply replacing recognition elements of proximity probes.

Peroxidase-mimicking DNAzyme modulated growth of CdS nanocrystalline structures in situ through redox reaction: application to development of genosensors and aptasensors

This work demonstrates the use of the peroxidase-mimicking DNAzyme (peroxidase-DNAzyme) as general and inexpensive platform for development of fluorogenic assays that do not require organic fluorophores. The system is based on the affinity interaction between the peroxidase-DNAzyme bearing hairpin sequence and the analyte (DNA or low molecular weight molecule), which changes the folding of the hairpin structure and consequently the activity of peroxidase-DNAzyme. Hence, in the presence of the analyte the peroxidase-DNAzyme structure is disrupted and does not catalyze the aerobic oxidation of l-cysteine to cystine. Thus, l-cysteine is not removed from the system and the fluorescence of the assay increases due to the in situ formation of fluorescent CdS nanocrystals. The capability of the system as a platform for fluorogenic assays was demonstrated through designing model geno- and aptasensor for the detection of a tumor marker DNA and a low molecular weight analyte, adenosine 5'triphosphate (ATP), respectively.

An improved G-quadruplex DNAzyme for dual-functional electrochemical biosensing of adenosines and hydrogen peroxide from cancer cells

A dual-functional electrochemical biosensor for adenosines and hydrogen peroxide from cancer cells was developed based on a traditional switchable electrochemical sensing format and ATP improved G-quadruplex DNAzyme as a biolabel.

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 DNA origami nanorobot controlled by nucleic acid hybridization

A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators.

Aptamer binding assays for proteins: the thrombin example--a review

Experimentally selected single-stranded DNA and RNA aptamers are able to bind to specific target molecules with high affinity and specificity. Many analytical methods make use of affinity binding between the specific targets and their aptamers. In the development of these methods, thrombin is the most frequently used target molecule to demonstrate the proof-of-principle. This paper critically reviews more than one hundred assays that are based on aptamer binding to thrombin. This review focuses on homogeneous binding assays, electrochemical aptasensors, and affinity separation techniques. The emphasis of this review is placed on understanding the principles and unique features of the assays. The principles of most assays for thrombin are applicable to the determination of other molecular targets.