A novel enzyme-free and label-free fluorescence aptasensor for amplified detection of adenosine

Label-free ratiometric fluorescence detection of Pb2+via structure-specific fluorescent dyes and dual signal amplification

Lead ions (Pb2+) are a widely distributed and highly toxic heavy metal pollutant, which seriously threatens the environment, economy and human safety. Here, a label-free ratiometric fluorescent biosensor was constructed for Pb2+ detection using DNAzyme-driven target cycling and exonuclease III (Exo III)-mediated DNA cycling as a dual signal amplification strategy. The SYBR Green I (SGI) and N-methyl mesoporphyrin IX (NMM) used in this study are characterized by low cost, storage resistance, and short preparation time compared with conventional signaling probes labeled with fluorescent groups. Unlike the single-emission fluorescence strategy, monitoring the fluorescence intensity ratio of SGI and NMM can effectively reduce external interference to achieve accurate detection of Pb2+. DNAzyme structures on the surface of magnetic beads (MBs) can recognize Pb2+ and activate the target circulatory system to cleave single-stranded DNA (ssDNA). The ssDNA further initiated the Exo III-assisted DNA circulatory system to digest double-stranded DNA (dsDNA) and release guanine-rich G1. Finally, the fluorescence signals of SGI and NMM were weakened and enhanced, respectively. The sensing strategy achieved a wide linear range from 0.5 to 500 nM and a low limit of detection (LOD) of 26.4 pM. Furthermore, its anti-interference ability and potential applicability for Pb2+ detection in actual samples were verified. This work ingeniously combines the dual signal amplification strategy with the ratiometric sensing strategy constructed by structure-specific fluorescent dyes, which provides a promising method for constructing sensitive and accurate fluorescent biosensors.

Targeted Selection of Aptamer Complementary Elements toward Rapid Development of Aptamer Transducers

Biosensing using aptamers has been a recent interest for their versatility in detecting many different analytes across a wide range of applications, including medical and environmental applications. In our last work, we introduced a customizable aptamer transducer (AT) that could successfully feed-forward many different output domains to target a variety of reporters and amplification reaction networks. In this paper, we explore the kinetic behavior and performance of novel ATs by modifying the aptamer complementary element (ACE) chosen based on a technique for exploring the ligand-binding landscape of duplexed aptamers. Using published data, we selected and constructed several modified ATs that contain ACEs with varying length, position of the start sites, and position of single mismatches, whose kinetic responses were tracked with a simple fluorescence reporter. A kinetic model for ATs was derived and used to extract the strand-displacement reaction constant k₁ and the effective aptamer dissociation constant K_d,eff, allowing us to calculate a relative performance metric, k₁/K_d,eff. Comparing our results with the predictions based on the literature data, we provide useful insight into the dynamics of the adenosine AT's duplexed aptamer domain and suggest a high-throughput approach for future ATs to be developed with improved sensitivity. The performance of our ATs showed a moderate correlation to those predicted by the ACE scan method. Here, we find that predicted performance based on our ACE selection method was moderately correlated to our AT's performance.

A simple tag-free fluorometric aptasensing assay for sensitive detection of kanamycin

A novel label-free and enzyme-free fluorescence aptasensing assay that uses Sybr Green I (SGI) as the signal indicator for the kanamycin determination was designed. An aptamer-complementary strand (Apt/CP) conjugate was formed, which provided the intercalation sites for SGI and, therefore, a considerable fluorescent signal. The introduction of the target led to the separation of Apt from CP due to the high affinity of Apt toward kanamycin. Hence, the suitable intercalation gaps reduced, which resulted in a decrease in the generated fluorescent signal. Under optimized conditions, a broad linear concentration range from 0.05 μM to 20 μM and a limit of detection of 11.76 nM were obtained, confirming the ability of the fabricated aptasensor for sensitive and specific kanamycin detection in real samples such as milk and human serum. The aptasensing method has the potential to be extensively employed in the food industry and veterinary science due to its simplicity, sensitivity, user-friendly, and capability of on-site detection of kanamycin.

A tag-free fluorescent aptasensor for tobramycin detection using a hybridization of three aptamer strands and SYBR Green I dye

In this study, a sensitive fluorescent method is designed to detect tobramycin (TOB) drug applying a hybrid structure of three aptamer strands and SYBR Green I (SGI) fluorescent dye as the bioreceptor segment and signal indicator, respectively. The preferential binding of the aptamers to TOB resulted in the collapse of the hybridized aptamer skeleton to the single strands. So, the intercalation of SGI molecules reduced that quenched the fluorescence response. The aptasensing assay provided the superior target specificity with a detection limit (LOD) of 0.153 pM and a wide linear dynamic range over 0.5 pM-300 μM. The aptasensor could successfully quantify TOB in human serum samples. The tag-free sensor with the remarkable advantages of simplicity, easy-to-use, cost-effectiveness, and high sensitivity is superior to be applicable for clinical samples.

Determination of adenosine by CRISPR-Cas12a system based on duplexed aptamer and molecular beacon reporter linked to gold nanoparticles

Adenosine as a potential tumor marker is of great value for clinical disease diagnosis. Since the CRISPR-cas12a system is only capable of recognizing nucleic acid targets we expanded the CRISPR-cas12a system to determine small molecules by designing a duplexed aptamer (DA) converting g-RNA recognition of adenosine to recognition of aptamer complementary DNA strands (ACD). To further improve the sensitivity of determination, we designed a molecule beacon (MB)/gold nanoparticle (AuNP)-based reporter, which has higher sensitivity than traditional ssDNA reporter. In addition, the AuNP-based reporter enables more efficient and fast determination. The determination of adenosine under 488-nm excitation can be realized within 7 min, which is more than 4 times faster than traditional ssDNA reporter. The linear determination range of the assay to adenosine was 0.5-100 μM with the determination limit of 15.67 nM. The  assay was applied to recovery determination of adenosine in serum samples with satisfactory results. The recoveries were between 91 and 106% and the RSD values of different concertation were below  4.8%. This sensitive, highly selective, and stable sensing system is expected to play a role in the clinical determination of adenosine and other biomolecules.

Improving the robustness of a catalyzed hairpin assembly with a three-arm nanostructure for nonenzymatic signal amplification

A nonenzymatic and isothermal signal amplification was performed by a 3-arm structure based on a catalyzed hairpin DNA assembly (3-CHA). By suppressing the leakage pathway, the sensitivity (<30 pM LOD) and selectivity of the 3-CHA were improved.

Facile design of multifunction-integrated linear oligonucleotide probe with multiplex amplification effect for label-free and highly sensitive GMO biosensing

Well-defined structures and compositions of nucleic acids afford oligonucleotide probes with unique chemical properties and biological functions for various biosensing applications. Herein, a unique and special oligonucleotide probe, named multifunction-integrated linear oligonucleotide probe (MI-LOP), was facile designed and reported for label-free and turn-on fluorescent detection of the codon component of genetically modified organisms (GMOs). The MI-LOP contains four different functional regions including recognition of target, serving as polymerization template, and creating polymerization primer-linked G-quadruplex (PP-G-quadruplex). Without the aid of any other oligonucleotides, the introduction of target DNA can make each function of the MI-LOP executed one-by-one, during which the species of target DNA, target analogue, and PP-G-quadruplex can be cyclically utilized and in turn induce a multiplex signal amplification responsible for substantial collection of the G-quadruplex moieties under isothermal conditions. The stable G-quadruplexes can combine with N-methyl mesoporphyrin IX (NMM) and function as efficient fluorescence light-up probes, rapidly leading to a dramatic increase in the fluorescence intensity for the amplified detection of the target codon component. Our results strongly demonstrate that the developed MI-LOP with multiplex amplification effect confers the sensing strategy a high sensitivity and specificity for quantitative and qualitative detection of the target codon. And it has also been successfully applied for analyzing target codon in the complex extractions of soybean. The achievements highlight the significance of using oligonucleotide probes as promising analytical tools to promote the basic biochemical research and help in food and environmental analysis.

Customizable Aptamer Transducer Network Designed for Feed-Forward Coupling

Solution-based biosensors that utilize aptamers have been engineered in a variety of formats to detect a range of analytes for both medical and environmental applications. However, since aptamers have fixed base sequences, incorporation of aptamers into DNA strand displacement networks for feed-forward signal amplification and processing requires significant redesign of downstream DNA reaction networks. We designed a novel aptamer transduction network that releases customizable output domains, which can then be used to initiate downstream strand displacement reaction networks without any sequence redesign of the downstream reaction networks. In our aptamer transducer (AT), aptamer input domains are independent of output domains within the same DNA complex and are reacted with a fuel strand after aptamer-ligand binding. ATs were designed to react with two fluorescent dye-labeled reporter complexes to show the customizability of the output domains, as well as being used as feed-forward inputs to two previously studied catalytic reaction networks, which can be used as amplifiers. Through our study, we show both successful customizability and feed-forward capability of our ATs.

A Non-Enzyme and Non-Label Sensitive Fluorescent Aptasensor Based on Simulation-Assisted and Target-Triggered Hairpin Probe Self-Assembly for Ochratoxin a Detection

The monitoring and control of mycotoxins has caused widespread concern due to their adverse effects on human health. In this research, a simple, sensitive and non-label fluorescent aptasensor has been reported for mycotoxin ochratoxin A (OTA) detection based on high selectivity of aptamers and amplification of non-enzyme hybridization chain reaction (HCR). After the introduction of OTA, the aptamer portion of hairpin probe H1 will combine with OTA to form OTA-aptamer complexes. Subsequently, the remainder of the opened H1 will act as an initiator for the HCR between the two hairpin probes, causing H1 and H2 to be sequentially opened and assembled into continuous DNA duplexes embedded with numerous G-quadruplexes, leading to a significant enhancement in fluorescence signal after binding with N-methyl-mesoporphyrin IX (NMM). The proposed sensing strategy can detect OTA with concentration as low as 4.9 pM. Besides, satisfactory results have also been obtained in the tests of actual samples. More importantly, the thermodynamic properties of nucleic acid chains in the monitoring platform were analyzed and the reaction processes and conditions were simulated before carrying out biological experiments, which theoretically proved the feasibility and simplified subsequent experimental operations. Therefore, the proposed method possess a certain application value in terms of monitoring mycotoxins in food samples and improving the quality control of food security.

A novel portable biosensor based on aptamer functionalized gold nanoparticles for adenosine detection

Adenosine has received great attentions acting as a potential biomarker for monitoring lung cancer. Most of the reported studies for adenosine detection require large instruments and complicated procedures. Herein, a sensitive, rapid and in-situ colorimetric aptasensor was developed for adenosine detection. Moreover, a homemade biomimetic electronic-eye (E-eye) was established and utilized as a portable in-time detection equipment. The entire measurement can be completed within 20 min, including the combination of aptamer with adenosine or AuNPs and the detection of adenosine. Four different kinds of aptamer were compared and the results showed that the AuNPs-aptamer-biotin system was the most stable and with the widest detection range of 5.0 μM-60.0 μM and the lowest LOD of 0.17 μM. Moreover, the artificial urine samples were also tested with a linear range from 5.0 to 50.0 μM and a LOD of 0.48 μM. The results validated that the aptasensor together with the E-eye can be a promising platform for adenosine detection.

An Enzyme- and Label-Free Fluorescence Aptasensor for Detection of Thrombin Based on Graphene Oxide and G-Quadruplex

An enzyme- and label-free aptamer-based assay is described for the determination of thrombin. A DNA strand (S) consisting of two parts was designed, where the first (Sa) is the thrombin-binding aptamer and the second (Se) is a G-quadruplex. In the absence of thrombin, Sa is readily adsorbed by graphene oxide (GO), which has a preference for ss-DNA rather than for ds-DNA. Upon the addition of the N-methyl-mesoporphyrin IX (NMM), its fluorescence (with excitation/emission at 399/610 nm) is quenched by GO. In contrast, in the presence of thrombin, the aptamer will bind thrombin, and thus, be separated from GO. As a result, fluorescence will be enhanced. The increase is linear in the 0.37 µM to 50 µM thrombin concentration range, and the detection limit is 0.37 nM. The method is highly selective over other proteins, cost-effective, and simple. In our perception, it represents a universal detection scheme that may be applied to other targets according to the proper choice of the aptamer sequence and formation of a suitable aptamer-target pair.

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme-free, high-efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single-stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in-depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000-fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.

The clinical application of purine nucleosides as biomarkers of tissue Ischemia and hypoxia in humans in vivo

During periods of ischemia and hypoxia, intracellular adenosine triphosphate stores are rapidly depleted. Its metabolism results in release of purine nucleosides into the systemic circulation. While the potential of purine nucleosides as a biomarker of ischemia has long been recognized, this has been limited by their complex physiological role and inherent instability leading to problematic sampling and prolonged, complex analysis procedures. Purine release has been demonstrated from cerebral tissue in patients undergoing carotid endarterectomy and patients presenting to hospital with stroke and transient ischemic attack. Rises in purine nucleosides have also been demonstrated in patients with angina and myocardial infarction, during systemic hypoxia, exercise, in patients with peripheral arterial disease and during surgery. This article reviews purine nucleoside production in ischemia, the development of purine analysis technology and details results of the studies investigating purine nucleosides as a biomarker of ischemia with suggestions for areas of future research.

Zero background and triple-signal amplified fluorescence aptasensor for antibiotics detection in foods

It's important to eliminate matrix interference for accurate detecting antibiotic residues in complex food samples. In this study, we designed a zero-backgrounded fluorescence aptasensor to achieve on-site detection of antibiotic residues, with chloramphenicol (CAP) as representative analyte. Moreover, a three stir-bars assisted target recycling system (TSBTR) was designed to achieve triple signal amplification and increase the sensitivity. The bars included one magnetic stir-bar modified with two kinds of long DNA chains, and two gold stir-bars modified with Y shape-duplex DNA probes respectively. In the presence of CAP, the target could recurrently react with the probes on the bars and replace a large amount of long DNA chains into supernatant. After then, the bars were taken out and SYBR green dye was added to the solution. The dye can specifically intercalate into the duplex structures of DNA chains to emit fluorescence while not emitting a signal in its free state. Under the optimized experimental conditions, a wide linear response range of 5 orders of magnitude from 0.001 ng mL^-1 to 10 ng mL^-1 was achieved with a detection limit of 0.033 pg mL^-1 CAP. The assay was successfully employed to detect CAP in food samples (milk & fish) with consistent results with ELISA's. High selectivity and sensitivity were attributed to the zero background signal and triple signal-amplification strategy. Moreover, the detection time can be shortened to 40 min due to that three signal amplified process can occur simultaneously. The fluorescent aptasensor was also label- and enzyme-free. All these ensure the platform to be rapid, cost-effective, easily-used, and is especially appropriate for detection antibiotics in food safety.

A ratiometric nanoprobe for biosensing based on green fluorescent graphitic carbon nitride nanosheets as an internal reference and quenching platform

The integrating of high fluorescent quenching capability of two-dimensional nanomaterials with dye-labelled ssDNA as nanoprobes has attracted increasing interest for biosensing applications. However, this absolute intensity-dependent single fluorescent signal may be influenced by target concentration-independent factors. To overcome this challenge, a ratiometric nanoprobe was developed by utilizing green fluorescent phenyl-doped carbon nitride (PDCN) nanosheets as an internal reference and quenching platform. 5-carboxy-X-rhodamine-labelled anti-adenosine aptamer was used as a signal probe. PDCN nanosheets quenched the fluorescence of the absorbed signal probe while kept their own fluorescence constantly. Upon addition of adenosine, the formation of adenosine-aptamer complexes led to desorption of the signal probe from the surface of PDCN nanosheets, resulted in the fluorescent recovery of the signal probe. The ratio of the fluorescent enhancement of the signal probe to the inherent fluorescence of PDCN nanosheets was used to quantitatively measure adenosine. The limit of detection for adenosine was 6.86 μM. Finally, the ratiometric nanoprobe was applied to determine adenosine in serum samples.

Label-free optical biosensor for target detection based on simulation-assisted catalyzed hairpin assembly

The development of efficient and convenient strategy without involving enzyme or complex nanomaterial for the micro molecules detection has profound meaning in the diagnosis of diseases. Herein, taking the advantages of the strong affinity of aptamer and catalyzed hairpin assembly, we develop a new non-label optical amplified strategy for thrombin detection in this work. To support both biological inquiry and technological innovation, thermodynamic models are introduced to predict the minimum energy secondary structure of interacting nucleic acid strands and calculate the partition function and equilibrium concentration for complexes in our system. Then, the thermodynamics properties of interacting DNA strands and the reactions of toehold strand displacement-driven assembly have been simulated, validating the feasibility of the theory and optimizing the follow-up lab tests. Following that, our strategy for thrombin detection is proved to be feasible and effective in biological experiment. Taken together, such a biosensor has a good potential in bioactive molecules detection and disease diagnosis for future biological research.

Graphene quantum dots-based electrochemiluminescence detection of DNA using multiple cycling amplification strategy

In this study, a novel strategy for amplified electrochemiluminescence (ECL) detection of DNA was proposed based on excellent ECL activity of graphene quantum dots (GQDs) coupled with multiple cycling amplification technique. A new type of graphene QDs with well ECL property and uniform size were firstly synthesized, then the graphene QDs were assembled on the electrode by poly (diallyldimethylammonium chloride) (PDDA)-graphene oxide (GO) nanocomposites, which could greatly improve ECL signal and stability of QDs. A novel signal-on ECL biosensor for DNA analysis was designed by using ECL quenching of gold nanoparticles (NPs) to graphene QDs combined with endonuclease-aided cyclic amplification strategy. As a result, the proposed strategy can be conveniently expanded to other biosensing application, especially in clinical diagnoses.

A Non-Label and Enzyme-Free Sensitive Detection Method for Thrombin Based on Simulation-Assisted DNA Assembly

Taking advantage of the high selectivity of aptamers and enzyme-free catalyzed hairpin assembly (CHA) amplification strategy, we herein describe a label-free and enzyme-free sensitive fluorescent and colorimetric strategy for thrombin detection in this paper. In the presence of target, the corresponding aptamer of the partial dsDNA probes will bind to the target and liberate the initiation strand, which is artfully designed as the “on” switch for hairpin assembly. Moreover, the displaced initiation strand partakes in a multi-cycle process and produces numerous G-quadruplexes, which have a remarkable enhancement in fluorescent/colorimetric signal from NMM (N-methyl-mesoporphyrin IX) and TMB (3,3′,5,5′-tetramethylbenzidine), respectively. The proposed amplification strategy for thrombin detection is of high sensitivity, down to 2.4 pM, and also achieves colorimetric signals that are able to be distinguished by naked eye. More importantly, the thermodynamics of interacting DNA strands used in our work, and the process of toehold strand displacement-driven assembly are simulated before biological testing, verifying the feasibility theoretically, and simplifying the subsequent actual experiments. Therefore, our approach and simulation have a certain potential application in biomarker detection and quantitatively monitor for disease diagnosis.

Equipment-Free Quantitative Aptamer-Based Colorimetric Assay Based on Target-Mediated Viscosity Change

In this paper, we describe an aptamer-based colorimetric assay (ABCA), which integrates enzyme-loaded microparticles for signal amplification with distance measurement for equipment-free quantitative readout. The distance measurement readout is on the basis of target-induced selective reduction in viscosity of reaction solution. Its utility is well demonstrated with inexpensive, sensitive, and selective detection of adenosine (model analyte) in buffer samples and real samples of human serum and urine with the naked eye. This ABCA method just requires operators to simply count the number of colored distance-relevant marked bars on the calibrated glass microsyringes (testing containers) to provide quantitative results. It thus holds great promise for wide applications particularly in limited-resource settings.

A reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue to DNA with alternating AT base sequence for sensitive detection of adenosine

We develop a reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue (MB) to DNA with alternating AT base sequence for sensitive detection of adenosine. We design a strand 1 with MB-modified thymine (T) base in the proximal 3' termini as the capture probe for its immobilization on the gold electrode and a 3' termini ferrocene (Fc)-modified aptamer for the recognition of adenosine. The hybridization of strand 1 with the aptamer leads to the formation of a double-stranded DNA (dsDNA) and consequently the away of MB from the electrode surface and the close of Fc to the electrode surface, generating a small value of I_MB/I_Fc (I_MB and I_Fc are the peak currents of MB and Fc, respectively). In the presence of adenosine, its binding with the aptamer induces the release of Fc from the electrode surface and the close of MB to the electrode surface, generating a large value of I_MB/I_Fc. As a result, adenosine may be accurately quantified by the measurement of ratiometric signal (I_MB/I_Fc). This ratiometric electrochemical biosensor can be simply fabricated and exhibits high sensitivity with a limit of detection of as low as 90.8pM and a large dynamic range from 0.1nM to 100μM. Moreover, this biosensor demonstrates good performance with excellent selectivity, regeneration capability, high reliability and good reproducibility, and may become a universal platform for the detection of various biomolecules which can be recognized by aptamers, holding great potential for further applications in biomedical research and clinical diagnosis.

A label-free and enzyme-free signal amplification strategy for a sensitive RNase H activity assay

We herein describe a label-free and enzyme-free signal amplification strategy for the sensitive determination of ribonuclease H (RNase H) activity, which relies on the target-triggered catalytic hairpin assembly (CHA) in conjunction with a G-quadruplex specific fluorescent binder, N-methyl mesoporphyrin IX (NMM). In the absence of RNase H, the RNA/DNA duplex serving as a substrate for RNase H cannot initiate the execution of CHA that produces G-quadruplexes; so NMM shows a low fluorescence signal. In contrast, the presence of RNase H that degrades RNA in the RNA/DNA duplex releases DNA designed to function as the catalyst for CHA. This consequently promotes the efficient CHA and generates a large number of G-quadruplexes with a significantly enhanced fluorescence signal from NMM. Based on this label-free and enzyme-free signal amplification strategy, we successfully determined the RNase H activity with a detection limit of 0.037 U mL^-1 and screened potential RNase H inhibitors. Our results suggest that the developed system is a promising platform for a cost-effective, sensitive enzyme activity assay and inhibitor screening.

Novel label-free and high-throughput microchip electrophoresis platform for multiplex antibiotic residues detection based on aptamer probes and target catalyzed hairpin assembly for signal amplification

Novel label-free and multiplex aptasensors have been developed for simultaneous detection of several antibiotics based on a microchip electrophoresis (MCE) platform and target catalyzed hairpin assembly (CHA) for signal amplification. Kanamycin (Kana) and oxytetracycline (OTC) were employed as models for testing the system. These aptasensors contained six DNA strands termed as Kana aptamer-catalysis strand (Kana apt-C), Kana inhibit strand (Kana inh), OTC aptamer-catalysis strand (OTC apt-C), OTC inhibit strand (OTC inh), hairpin structures H1 and H2 which were partially complementary. Upon the addition of Kana or OTC, the binding event of aptamer and target triggered the self-assembly between H1 and H2, resulting in the formation of many H1-H2 complexes. They could show strong signals which represented the concentration of Kana or OTC respectively in the MCE system. With the help of the well-designed and high-quality CHA amplification, the assay could yield 300-fold amplified signal comparing that from non-amplified system. Under optimal conditions, this assay exhibited a linear correlation in the ranges from 0.001ngmL^-1 to 10ngmL^-1, with the detection limits of 0.7pgmL^-1 and 0.9pgmL^-1 (S/N=3) toward Kana and OTC, respectively. The platform has the following advantages: firstly, the aptamer probes can be fabricated easily without labeling signal tags for MCE detection; Secondly, the targets can just react with probes and produce the amplified signal in one-pot. Finally, the targets can be simultaneously detected within 10min in different channels, thus high-throughput measurement can be achieved. Based on this work, it is estimated that this detection platform will be universally served as a simple, sensitive and portable platform for antibiotic contaminants detection in biological and environmental samples.

Enzyme-free, signal-amplified nucleic acid circuits for biosensing and bioimaging analysis

Enzyme-free, signal-amplified nucleic acid circuits utilize programmed assembly reactions between nucleic acid substrates to transduce a chemical input into an amplified detection signal.

A catalytic assembled enzyme-free three-dimensional DNA walker and its sensing application

A novel and enzyme-free three-dimensional DNA walker powered by catalytic assembly has been constructed.

Self-locked aptamer probe mediated cascade amplification strategy for highly sensitive and selective detection of protein and small molecule

In this work, a novel self-locked aptamer probe mediated cascade amplification strategy has been constructed for highly sensitive and specific detection of protein. First, the self-locked aptamer probe was designed with three functions: one was specific molecular recognition attributed to the aptamer sequence, the second was signal transduction owing to the transduction sequence, and the third was self-locking through the hybridization of the transduction sequence and part of the aptamer sequence. Then, the aptamer sequence specific recognized the target and folded into a three-way helix junction, leading to the release of the transduction sequence. Next, the 3'-end of this three-way junction acted as primer to trigger the strand displacement amplification (SDA), yielding a large amount of primers. Finally, the primers initiated the dual-exponential rolling circle amplification (DE-RCA) and generated numerous G-quadruples sequences. By inserting the fluorescent dye N-methyl mesoporphyrin IX (NMM), enhanced fluorescence signal was achieved. In this strategy, the self-locked aptamer probe was more stable to reduce the interference signals generated by the uncontrollable folding in unbounded state. Through the cascade amplification of SDA and DE-RCA, the sensitivity was further improved with a detection limit of 3.8 × 10(-16) mol/L for protein detection. Furthermore, by changing the aptamer sequence of the probe, sensitive and selective detection of adenosine has been also achieved, suggesting that the proposed strategy has good versatility and can be widely used in sensitive and selective detection of biomolecules.

An electrochemical aptasensor based on TiO2/MWCNT and a novel synthesized Schiff base nanocomposite for the ultrasensitive detection of thrombin

A sensitive aptasensor based on a robust nanocomposite of titanium dioxide nanoparticles, multiwalled carbon nanotubes (MWCNT), chitosan and a novel synthesized Schiff base (SB) (TiO2/MWCNT/CHIT/SB) on the surface of a glassy carbon electrode (GCE) was developed for thrombin detection. The resultant nanocomposite can provide a large surface area, excellent electrocatalytic activity, and high stability, which would improve immobilization sites for biological molecules, allow remarkable amplification of the electrochemical signal and contribute to improved sensitivity. Thrombin aptamers were simply immobilized onto the TiO2-MWCNT/CHIT-SB nanocomposite matrix through simple π - π stacking and electrostatic interactions between CHIT/SB and aptamer strands. The electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were used to analyze the surface characterization of unmodified GCE and TiO2-MWCNT/CHIT-SB modified GCE, and also the interaction between aptamer and thrombin. In the presence of thrombin, the aptamer on the adsorbent layer captures the target on the electrode interface, which makes a barrier for electrons and inhibits electron transfer, thereby resulting in decreased DPV and increased impedance signals of the TiO2-MWCNT/CHIT-SB modified GCE. Furthermore, the proposed aptasensor has a very low LOD of 1.0fmolL(-1) thrombin within the detection range of 0.00005-10nmolL(-1). The aptasensor also presents high specificity and reproducibility for thrombin, which is unaffected by the coexistence of other proteins. Clinical application was performed with analysis of the thrombin levels in blood and CSF samples obtained from patients with MS, Parkinson, Epilepsy and Polyneuropathy using both the aptasensor and commercial ELISA kit. The results revealed the proposed system to be a promising candidate for clinical analysis of thrombin.

Development of a luminescent G-quadruplex-selective iridium(III) complex for the label-free detection of adenosine

A panel of six luminescent iridium(III) complexes were synthesized and evaluated for their ability to act as G-quadruplex-selective probes. The novel iridium(III) complex 1 was found to be highly selective for G-quadruplex DNA, and was employed for the construction of a label-free G-quadruplex-based adenosine detection assay in aqueous solution. Two different detection strategies were investigated for adenosine detection, and the results showed that initial addition of adenosine to the adenosine aptamer gave superior results. The assay exhibited a linear response for adenosine in the concentration range of 5 to 120 μM (R(2) = 0.992), and the limit of detection for adenosine was 5 μM. Moreover, this assay was highly selective for adenosine over other nucleosides, and exhibited potential use for biological sample analysis.

Aptasensor based on fluorescence resonance energy transfer for the analysis of adenosine in urine samples of lung cancer patients

A new aptasensor was designed for the analysis of adenosine based on fluorescence resonance energy transfer (FRET) between CdS quantum dot (QDs) as a donor and polypyrrole (Ppy) as an acceptor. The QDs were covalently bonded to anti-adenosine aptamer where its fluorescence was quenched by Ppy. When Ppy was replaced by adenosine, the fluorescence of QDs was restored and its intensity was proportional to the adenosine concentration. Under the optimized conditions, a linear range was found to be 23-146 nM with a detection limit of 9.3 nM. The method was used for analysis of adenosine in urine samples of lung cancer patients and its accuracy was evaluated by comparison of the results of the proposed method with the standard method of HPLC-UV. Furthermore, the interactions of adenosine molecules with the aptamer were investigated using molecular modeling, including molecular dynamic simulations (MDS). The results demonstrated that each G-quadruplex aptamer can capture two adenosine molecules.

A universal label-free fluorescent aptasensor based on Ru complex and quantum dots for adenosine, dopamine and 17β-estradiol detection

Based on specific aptamer binding properties, a strategy for adenosine, dopamine and 17β-estradiol detection was realised by employing Ru complex and quantum dots (QDs) as fluorescence probes. Ru complex, which could quench the fluorescence of QDs, preferred to bind with aptamer DNA and resulted in the fluorescence rise of QDs. When the aptamer DNA was incubated with the target first, it could not bind with Ru complex and the fluorescence of QDs was quenched. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of adenosine, dopamine and 17β-estradiol with a limit of detection (LOD) of 101 nM, 19 nM and 37 nM, respectively. The experiments in fetal bovine serum were also carried out with good results. This universal method was rapid, label-free, low-cost, easy-operating and highly repeatable for the detection of adenosine, dopamine and 17β-estradiol. Qualitative detection by naked eyes was also available without complex instruments. It could also be extended to detect various analytes, such as metal ions, proteins and small molecules by using appropriate aptamers.

An electrochemical aptasensor based on a TiO2/three-dimensional reduced graphene oxide/PPy nanocomposite for the sensitive detection of lysozyme

A sensitive aptasensor based on a nanocomposite of hollow titanium dioxide nanoball, three-dimensional reduced graphene oxide, and polypyrrole (TiO2/3D-rGO/PPy) was developed for lysozyme detection. A lysozyme aptamer was easily immobilized onto the TiO2/3D-rGO/PPy nanocomposite matrix by assembling the aptamer onto graphene through simple π-stacking interactions and electrostatic interactions between PPy molecular chains and aptamer strands. In the presence of lysozyme, the aptamer on the adsorbent layer catches the target on the electrode interface, which generates a barrier for electrons and inhibits electron transfer, subsequently resulting in decreased electrochemically differential pulse voltammetric signals of a gold electrode modified with TiO2/3D-rGO/PPy. Using this strategy, a low limit of detection of 0.085 ng mL(-1) (5.5 pM) for detecting lysozyme was observed within the detection range of 0.1-50 ng mL(-1) (0.007-3.5 nM). The aptasensor also presents high specificity for lysozyme, which is unaffected by the coexistence of other proteins. Such an aptasensor opens a rapid, selective, and sensitive route to lysozyme detection. This finding indicates that the TiO2/3D-rGO/PPy nanocomposite could be used as an electrochemical biosensor for detecting proteins in the biomedical field.

A graphene oxide-based enzyme-free signal amplification platform for homogeneous DNA detection

A graphene oxide (GO) based enzyme-free signal amplification platform for homogeneous DNA sensing is developed with simplicity and high sensitivity. In the absence of the target DNA, labeled hairpin probe 1 (H1) and probe 2 (H2) were adsorbed on the surface of GO, resulting in the fluorescence quenching of the dyes and minimizing the background fluorescence. The addition of the target DNA facilitated the formation of double-stranded DNA (dsDNA) between H1 and H2, causing the probes to separate from GO and release the target DNA through a strand displacement reaction. Meanwhile, the whole reaction started anew. This is an excellent isothermal signal amplification technique without the involvement of enzymes. By monitoring the change of the fluorescence intensity, the target DNA not only can be determined in buffer solution, but also can be detected in 1% serum solution spiked with a series of concentrations of the target DNA. In addition, the consumption amount of the probes in this method is lower than that in traditional molecular beacon methods.

Label-free aptasensor for adenosine deaminase sensing based on fluorescence turn-on

A label-free and fluorescence turn-on aptamer biosensor has been developed for the detection of adenosine deaminase (ADA) activity with simplicity and selectivity. Adenosine aptamer will form a tight stem-loop structure upon binding with adenosine. In the absence of ADA, only a small quantity of picagreen intercalates into the stem section of aptamer, resulting in a low fluorescence of picagreen when excited at 490 nm. Interestingly, after the addition of ADA, adenosine is hydrolyzed to inosine, and the released aptamer forms double-stranded DNA (dsDNA) with its complementary single-stranded DNAc, followed by the intercalation of picagreen to dsDNA. When the solution is excited, picagreen emits strong green fluorescence. The increased fluorescence intensity of picagreen is dependent on the concentration of ADA. The detection limit of the ADA is determined to be 2 U L(-1), which is lower than ADA cutoff value (4 U L(-1)) in the clinical requirement and more sensitive than most of the reported methods. Compared to other previous ADA sensors, the assay is not only label-free but also a turn-on signal, and possesses properties of lower cost and simpler detection system. Furthermore, this label-free strategy is also applicable to the assay of other enzymes and screening of corresponding inhibitors.

An enzyme-free strategy for ultrasensitive detection of adenosine using a multipurpose aptamer probe and malachite green

We report on an enzyme-free and label-free strategy for the ultrasensitive determination of adenosine. A novel multipurpose adenosine aptamer (MAAP) is designed, which serves as an effective target recognition probe and a capture probe for malachite green. In the presence of adenosine, the conformation of the MAAP is converted from a hairpin structure to a G-quadruplex. Upon addition of malachite green into this solution, a noticeable enhancement of resonance light scattering was observed. The signal response is directly proportional to the concentration of adenosine ranging from 75 pM to 2.2 nM with a detection limit of 23 pM, which was 100-10,000 folds lower than those obtained by previous reported methods. Moreover, this strategy has been applied successfully for detecting adenosine in human urine and blood samples, further proving its reliability. The mechanism of adenosine inducing MAAP to form a G-quadruplex was demonstrated by a series of control experiments. Such a MAAP probe can also be used to other strategies such as fluorescence or spectrophotometric ones. We suppose that this strategy can be expanded to develop a universal analytical platform for various target molecules in the biomedical field and clinical diagnosis.

A turn-on fluorescent aptasensor for adenosine detection based on split aptamers and graphene oxide

A simple, sensitive and selective turn-on fluorescent aptasensor for adenosine detection was developed based on target-induced split aptamer fragment conjunction and different interactions of graphene oxide and the two states of the designed aptamer sequences.

Hairpin assembly circuit-based fluorescence cooperative amplification strategy for enzyme-free and label-free detection of small molecule

Here, we developed an enzyme-free, label-free, and sensitive fluorescence cooperative amplification strategy based on a hairpin assembly circuit which coupled catalytic hairpin assembly (CHA) with hybridization chain reaction (HCR) for small molecule adenosine. A double-strand DNA probe with aptamer-catalysis strand (Apt-C) and inhibit strand (Inh) was designed for adenosine recognition and signal transduction which was named as Apt-C/Inh. Hairpins H1 and H2 were employed for constructing the CHA, and hairpins H3 and H4 for the HCR. Through the binding of adenosine and the Apt-C, the Inh was released from the Apt-C/Inh. Then the free Apt-C initiated the CHA through successively opening H1 and H2, generating H1/H2 complex and recyclable Apt-C. Next, the released Apt-C entered another CHA cycle, and the H1/H2 complex further initiated the HCR of H3 and H4 which induced the formation of the concatemers of H3/H4 complex. Such a process brought the two ends of hairpins H3 into close proximity, yielding numerous integrated G-quadruplexes which were initially sequestered in the stem and two terminals of H3. Finally, N-methyl mesoporphyrin IX (NMM) was added to generate an enhanced fluorescence signal. In the proposed strategy, driven only by the energy from hybridization, one target could trigger multiple HCR events via CHA-based target-cycle, leading to a remarkable enzyme-free amplification for adenosine. The detection limit could achieve as low as 9.7 × 10(-7) mol L(-1). Furthermore, G-quadruplexes were applied to construct label-free hairpin assembly circuit, which made it more simple and cost-effective. The satisfactory recoveries were obtained when detecting adenosine in spiked human serum and urine samples, demonstrating the feasibility of this detection strategy in biological samples.

Target-driven self-assembly of stacking deoxyribonucleic acids for highly sensitive assay of proteins

In this paper, we report a new signal amplification strategy for highly sensitive and enzyme-free method to assay proteins based on the target-driven self-assembly of stacking deoxyribonucleic acids (DNA) on an electrode surface. In the sensing procedure, binding of target protein with the aptamer probe is used as a starting point for a scheduled cycle of DNA hairpin assembly, which consists of hybridization, displacement and target regeneration. Following numbers of the assembly repeats, a great deal of DNA duplexes can accordingly be formed on the electrode surface, and then switch on a succeeding propagation of self-assembled DNA concatemers that provide further signal enhancement. In this way, each target binding event can bring out two cascaded DNA self-assembly processes, namely, stacking DNA self-assembly, and therefore can be converted into remarkably intensified electrochemical signals by associating with silver nanoparticle-based readout. Consequently, highly sensitive detection of target proteins can be achieved. Using interferon-gamma as a model, the assay method displays a linear range from 1 to 500 pM with a detection limit of 0.57 pM, which is comparable or even superior to other reported amplified assays. Moreover, the proposed method eliminates the involvement of any enzymes, thereby enhancing the feasibility in clinical diagnosis.

Enzymatic cleavage and mass amplification strategy for small molecule detection using aptamer-based fluorescence polarization biosensor

Fluorescence polarization (FP) assays incorporated with fluorophore-labeled aptamers have attracted great interest in recent years. However, detecting small molecules through the use of FP assays still remains a challenge because small-molecule binding only results in negligible changes in the molecular weight of the fluorophore-labeled aptamer. To address this issue, we herein report a fluorescence polarization (FP) aptamer assay that incorporates a novel signal amplification strategy for highly sensitive detection of small molecules. In the absence of adenosine, our model target, free FAM-labeled aptamer can be digested by nuclease, resulting in the release of FAM-labeled nucleotide segments from the dT-biotin/streptavidin complex with weak background signal. However, in the presence of target, the FAM-labeled aptamer-target complex protects the FAM-labeled aptamer from nuclease cleavage, allowing streptavidin to act as a molar mass amplifier. The resulting increase in molecular mass and FP intensity of the aptamer-target complex provides improved sensitivity for concentration measurement. The probe could detect adenosine from 0.5 μM to 1000 μM, with a detection limit of 500 nM, showing that the sensitivity of the probe is superior to aptamer-based FP approaches previously reported for adenosine. Importantly, FP could resist environmental interferences, making it useful for complex biological samples without any tedious sample pretreatments. Our results demonstrate that this dual-amplified, aptamer-based strategy can be used to design fluorescence polarization probes for rapid, sensitive, and selective measurement of small molecules in complicated biological environment.

Real-time monitoring of enzyme-free strand displacement cascades by colorimetric assays

The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications.

Label-free fluorescence dual-amplified detection of adenosine based on exonuclease III-assisted DNA cycling and hybridization chain reaction

In this work, we constructed a label-free and dual-amplified fluorescence aptasensor for sensitive analysis of adenosine based on exonuclease III (Exo III)-assisted DNA cycling and hybridization chain reaction (HCR). Firstly, we fabricated a trifunctional probe that consisting of the catalytic strand, the aptamer sequence and a streptavidin-magnetic nanobead (streptavidin-MNB). The streptavidin-MNB played a role of enrichment and separation to achieve a low background. The aptamer sequence was employed as a recognition element to bind the target adenosine, leading to the releasing of the catalytic stand. Then, the catalytic strand induced the Exo III-assisted DNA cycling reaction and produced a large amount of DNA fragments, which got a primary amplification. Subsequently, the DNA fragments acted as trigger strands to initiate HCR, forming nicked double helices with multiple G-quadruplex structures, which achieved a secondary amplification. Finally, the G-quadruplex structures bonded with the N-nethyl mesopor-phyrin IX (NMM) and yielded an enhanced fluorescence signal, realizing the label-free detection. In the proposed strategy, a small amount of adenosine can be converted to a large amount of DNA triggers, leading to a significant amplification for the target. This method exhibited a high sensitivity toward adenosine with a detection limit of 4.2×10(-7) mol L(-1), which was about 10 times lower than that of the reported label-free strategies. Moreover, this assay can significantly distinguish the content of adenosine in urine samples of cancer patients and normal human, indicating that our method will offer a new strategy for reliable quantification of adenosine in medical research and early clinical diagnosis.