Signal amplification by strand displacement in a carbon dot based fluorometric assay for ATP

A multifunctional fluorescent sensor for Ag+ and Hg2+ detection in seawater

In order to detect Ag+ and Hg2+ in seawater, we explored a multifunctional fluorescence sensor. A multifunctional Ag+ and Hg2+ sensor was designed by using gold nanoparticles (AuNPs) as quenching agent, PicoGreen dye as fluorescent probe of base pairing double-stranded deoxyribonucleic acid (DNA), and combining the characteristics of Ag+ making C base mismatch and Hg2+ making T base mismatch. Meanwhile, the DNA logic gate was constructed by establishing logic circuit, truth table, and logic formula. The relevant performances of the sensor were investigated. The results revealed that the sensor can detect Ag+ in the range of 100 to 700 nM with R2 = 0.98129, and its detection limit is 16.88 nM (3σ/slope). The detection range of Hg2+is 100-900 nM with R2 = 0.99725, and the detection limit is 5.59 nM (3σ/slope). An AND-AND-NOR-AND molecular logic gate has been successfully designed. With the characteristics of high sensitivity, multifunction, and low cost, the recommended detection method has the potential to be applied to the detection of Ag+ and Hg2+ in seawater.

Functional Nucleic Acid Probes Based on Two-Photon for Biosensing

Functional nucleic acid (FNA) probes have been widely used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging because of their easy synthesis, functional modification, flexible design, and stable properties. However, most FNA probes are designed based on one-photon (OP) in the ultraviolet or visible regions, and the effectiveness of these OP-based FNA probes may be hindered by certain factors, such as their potential for photodamage and limited light tissue penetration. Two-photon (TP) is characterized by the nonlinear absorption of two relatively low-energy photons of near-infrared (NIR) light with the resulting emission of high-energy ultraviolet or visible light. TP-based FNA probes have excellent properties, including lower tissue self-absorption and autofluorescence, reduced photodamage and photobleaching, and higher spatial resolution, making them more advantageous than the conventional OP-based FNA probes in biomedical sensing. In this review, we summarize the recent advances of TP-excited and -activated FNA probes and detail their applications in biomolecular detection. In addition, we also share our views on the highlights and limitations of TP-based FNA probes. The ultimate goal is to provide design approaches for the development of high-performance TP-based FNA probes, thereby promoting their biological applications.

Enhancing Electrochemical Biosensor Performance for 17β-Estradiol Determination with Short Split-Aptamers

Chronic exposure of 17β-estradiol (E2) even at low concentration can disorganize the endocrine system and lead to undesirable health problems in the long run. An electrochemical biosensor for rapid detection of E2 in water samples was successfully developed. The biosensor was based on split DNA aptamers attached onto poly (methacrylic acid-co-n butyl acrylate-succinimide) microspheres deposited on polypyrrole nanowires coated electrode (PPY/PMAA-NBA). The sandwich paired of split DNA aptamers used were truncated from 75 mer parent aptamers. These two strands of 12-mer and 14-mer split DNA aptamers were then immobilized on the PMAA-NBA microspheres. In the presence of E2, the split DNA aptamers formed an apt12-E2-apt14 complex, where the binding reaction on the electrode surface led to the detection of E2 by differential pulse voltammetry using ferrocyanide as a redox indicator. Under optimum conditions, the aptasensor detected E2 concentrations in the range of 1 × 10^-4 M to 1 × 10^-12 M (R² = 0.9772) with a detection limit of 4.8 × 10^-13 M. E2, which were successfully measured in a real sample with 97-104% recovery and showed a good correlation (R² = 0.9999) with the established method, such as high-performance liquid chromatography. Interactions between short and sandwich-type aptamers (split aptamers) demonstrated improvement in aptasensor performance, especially the selectivity towards several potential interferents.

Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection

The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.

Nano optical and electrochemical sensors and biosensors for detection of narrow therapeutic index drugs

For the first time, a comprehensive review is presented on the quantitative determination of narrow therapeutic index drugs (NTIDs) by nano optical and electrochemical sensors and biosensors. NTIDs have a narrow index between their effective doses and those at which they produce adverse toxic effects. Therefore, accurate determination of these drugs is very important for clinicians to provide a clear judgment about drug therapy for patients. Routine analytical techniques have limitations such as being expensive, laborious, and time-consuming, and need a skilled user and therefore  the nano/(bio)sensing technology leads to high interest.

Exo III-Catalyzed Release of a Zn2+-Ligation DNAzyme to Drive the Strand Displacement Reaction and Gold Aggregation for the Homogeneous Bioassay of Kanamycin Antibiotics

Herein, we combine the exonuclease III (Exo III)-catalyzed release of a Zn²⁺-dependent ligation DNAzyme with the DNAzyme-driven strand displacement reaction (SDR) to develop a novel homogeneous colorimetric bioassay method for kanamycin (Kana) antibiotic detection. Upon the biorecognition reaction between Kana and a designed hairpin DNA, the DNAzyme-containing strand can be catalytically released by Exo III. Then, this DNAzyme will catalyze the ligation of two oligonucleotides to cause a SDR and the aggregation of gold nanoparticles (Au NPs) labeled by two linker DNA strands. Due to the aggregation of Au NPs for colorimetric signal transduction and the Exo III and SDR-assisted dual signal amplification, this method shows a wide linear range of 5 orders of magnitude and a very low detection limit down to 8.1 fg mL^-1. Together with its excellent selectivity, repeatability, reliability, and convenient manipulation, the proposed method shows a great potential for the food quality monitoring application.

A magnified aptamer fluorescence sensor based on the metal organic frameworks adsorbed DNA with enzyme catalysis amplification for ultra-sensitive determination of ATP and its logic gate operation

With the development of frame materials, metal organic frameworks (MOFs) have been successfully applied in the fields of biological small molecule analysis and fluorescent DNA detection. In this work, in view of the good adsorption characteristics of MIL-101(Cr), the highly sensitive detection of adenosine triphosphate (ATP) assisted nucleic acid exonuclease amplification by MIL-101(Cr) on the different affinity of single stranded DNA and double stranded DNA was investigated. The detection limit of ATP reaches 1.7 μM, and the platform has good applicability in biological samples. On this basis, an "AND" logic gate was successfully constructed. Superior sensitivity to ATP in the presence of exonuclease was reflected, which greatly enhanced the system's fluorescence. Importantly, the fluorescence sensing application of this nanomaterial inspired other target detection and enriched the building blocks of fluorescence sensing platform.

Ultra-sensitive detection of ATP in serum and lysates based on nitrogen-doped carbon dots

In this work, novel types of nitrogen-doped carbon dots (N-CDs) were prepared from citric acid and glycine (GLY) as precursors through a simple pyrolysis method. The GLY-CDs showed strong fluorescence with a fluorescence quantum yield as high as 33.34% and good water solubility. The fluorescence of GLY-CDs could be selectively quenched by iron(III) ion (Fe³⁺ ) resulting in the non-fluorescent complex. Due to the high affinity of Fe³⁺ to adenosine-5'-triphosphate (ATP), the fluorescence of the GLY-CDs in GLY-CDs-Fe³⁺ could be recovered by ATP. Thereby, quantitatively fluorescent turn-on detection of ATP could be achieved. The fluorescence recovery ratio was linearly proportional to the concentration of ATP with a detection limit as low as 15.0 nM, indicating the CDs have high sensitivity. The GLY-CDs were successfully employed in the detection of ATP in serum and cell lysates.

Red pitaya peels-based carbon dots for real-time fluorometric and colorimetric assay of Au3+, cellular imaging, and antioxidant activity

The synthesis of fascinating multifunctional carbon dots (CDs) attracted immense attention. Here, a facile solvothermal treatment of red pitaya peels in acetic acid produced CDs (designated as ACDs, excitation/emission wavelengths at 357/432 nm). ACDs with high sp²-hybridized carbon and carboxylic group contents can rapidly and selectively reduce Au³⁺ to Au⁰, and stabilize produced Au nanoparticles (AuNPs). The synergetic effect of electron transfer from ACDs to Au³⁺ and inner filter effect (IFE) from ACDs to AuNPs quenches the fluorescence within 30 s. Simultaneously, the resulting AuNPs have a purple color with a maximum absorption at 545 nm for visual detection. Therefore, for the first time, we reported a fluorometric and colorimetric dual-mode sensing system for real-time, highly sensitive and selective detection of Au³⁺. The fluorescence quenching ratio and absorbance change linearly with the increase of Au³⁺ concentration in the range of 0.3-8.0 μM and 3.3-60.0 μM with limits of detection (LODs) at 0.072 μM and 2.2 μM, respectively. The assay was applied for Au³⁺ determination in spiked real water samples with recoveries from 95.5 to 105.0%, and relative standard deviation (RSD) of less than 6.5%. Furthermore, ACDs with good photostability, low cytotoxicity, and excellent biocompatibility were successfully applied for intracellular Au³⁺ sensing and imaging. In addition, ACDs exhibited an extraordinarily high antioxidant activity, with an IC₅₀ value for DPPH radical scavenging (0.70 μg mL^-1) much lower than that of ascorbic acid (4.34 μg mL^-1). The proposed strategy demonstrates the outstanding properties of ACDs in chemical and biomedical analysis. Graphical abstract.

Nanobiosensing with graphene and carbon quantum dots: Recent advances

Graphene and carbon quantum dots (GQDs and CQDs) are relatively new nanomaterials that have demonstrated impact in multiple different fields thanks to their unique quantum properties and excellent biocompatibility. Biosensing, analyte detection and monitoring wherein a key feature is coupled molecular recognition and signal transduction, is one such field that is being greatly advanced by the use of GQDs and CQDs. In this review, recent progress on the development of biotransducers and biosensors enabled by the creative use of GQDs and CQDs is reviewed, with special emphasis on how these materials specifically interface with biomolecules to improve overall analyte detection. This review also introduces nano-enabled biotransducers and different biosensing configurations and strategies, as well as highlights key properties of GQDs and CQDs that are pertinent to functional biotransducer design. Following relevant introductory material, the literature is surveyed with emphasis on work performed over the last 5 years. General comments and suggestions to advance the direction and potential of the field are included throughout the review. The strategic purpose is to inspire and guide future investigations into biosensor design for quality and safety, as well as serve as a primer for developing GQD- and CQD-based biosensors.

A molecular device: A DNA molecular lock driven by the nicking enzymes

As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.

Rapid and sensitive detection of Mycobacterium tuberculosis based on strand displacement amplification and magnetic beads

Tuberculosis is one of the main infectious diseases threatening public health, and the development of simple, rapid, and cost-saving methods for tuberculosis diagnosis is of profound importance for tuberculosis prevention and treatment. The bacterium Mycobacterium tuberculosis (MTB) is the pathogen that causes tuberculosis, and assaying for MTB is the only criterion for tuberculosis diagnosis. A new enzyme-free method based on strand displacement amplification and magnetic beads was developed for simple, rapid, and cost-saving MTB detection. Under optimum conditions, a good linear relationship could be observed between fluorescence and MTB specific DNA concentration ranging from 0.05 to 150 nM with a correlation coefficient of 0.993 (n = 8) and a detection limit of 47 pM (3σ/K). The present method also distinguished a one base mismatch from MTB specific DNA, showing great promise for MTB genome single base polymorphism analysis. MTB specific DNA content in polymerase chain reaction samples was successfully detected using the new method, and recoveries were 97.8-100.8%, indicating that the present method had high accuracy and shows good potential for the early diagnosis of tuberculosis.

Fluorescent Carbon Dots for in Situ Monitoring of Lysosomal ATP Levels

Monitoring the ATP levels in lysosomes in situ is crucial for understanding their involvement in various biological processes but remains difficult due to the interference of ATP in other organelles or the cytoplasm. Here, we report a lysosome-specific fluorescent carbon dot (CD), which can be used to detect ATP in acidic lysosomes with "off-on" changes of yellow fluorescence. These CDs were successfully applied in real-time monitoring of the fluctuating concentration of lysosomal ATP induced by drug stimulation (e.g., chloroquine, etoposide, and oligomycin). Because of the excellent specificity, these CDs are promising agents for drug screening and medical diagnostics through lysosomal ATP monitoring.

One-step and ultrasensitive ATP detection by using positively charged nano-gold@graphene oxide as a versatile nanocomposite

A versatile nanocomposite was simply prepared based upon the electrostatic adsorption of positively charged gold nanoparticles with negatively charged graphene oxide (nano-gold@GO), and utilized as a novel fluorescence quenching platform for ultrasensitive detection of adenosine triphosphate (ATP). In the designed system, DNA-stabilized Ag nanoclusters (DNA/AgNCs) were used as fluorescent probes, DNA duplex was formed in the presence of ATP, and they can electrostatically adsorb onto the surface of nano-gold@GO to quench the fluorescence signal. Upon the addition of exonuclease III (Exo III), the DNA duplex would be hydrolyzed into DNA fragments and resulted in the recovery of the fluorescence signals due to the diffusion of AgNCs away from nano-gold@GO. Based on these, sensitive detection of ATP was realized with a detection range of 5.0 pM-20 nM. Notably, a good recovery in the range of 94-104% was obtained when detecting ATP in human serum samples, indicating a promising application value in early disease diagnosis. Graphical abstract A functional positively charged nano-gold@graphene oxide was fabricated and utilized as an enhanced fluorescence quenching platform for the detection of ATP, coupled with exonuclease III-assisted signal amplification.

Using the NIH symptom science model to understand fatigue and mitochondrial bioenergetics

The symptom of fatigue is prevalent among patients with chronic diseases and conditions such as congestive heart failure and cancer. It has a significant debilitating impact on patients' physical health, quality of life, and well-being. Early detection and appropriate assessment of fatigue is essential for diagnosing, treating, and monitoring disease progression. However, it is often challenging to manage the symptom of fatigue without first investigating the underlying biological mechanisms. In this narrative review, we conceptualize the symptom of fatigue and its relationship with mitochondrial bioenergetics using the National Institute of Health Symptom Science Model (NIH-SSM). In particular, we discuss mental and physical measures to assess fatigue, the importance of adenosine triphosphate (ATP) in cellular and organ functions, and how impaired ATP production contributes to fatigue. Specific methods to measure ATP are described. Recommendations are provided concerning how to integrate biological mechanisms with the symptom of fatigue for future research and clinical practice to help alleviate symptoms and improve patients' quality of life.

Ultrasensitive and label-free detection of ATP by using gold nanorods coupled with enzyme assisted target recycling amplification

Abnormal concentration of adenosine triphosphate (ATP) is directly asscociate with several diseases. Thus, sensitive detection of ATP is essential to early diagnosis of disease. Herein, we described an ultrasensitive strategy for ATP detection by using positively charged gold nanorods ((+)AuNRs) as an efficient fluorescence quenching platform, coupled with exonuclease Ⅲ (Exo Ⅲ) assisted target recycling amplification. To construct the sensor, DNA template that contained ATP aptamer was used for the formation of Ag nanoclusters signal probe (DNA/AgNCs), the structure of it could change to duplex after the interaction of it with ATP. Such DNA template or duplex DNA product could electrostatically adsorb onto (+)AuNRs surface, resulting in the quenching of the fluorescence signal due to the vicinity of AgNCs to (+)AuNRs. With the addition of Exo Ⅲ, DNA duplex could be hydrolyzed and released from (+)AuNRs surface, leading to the recovery of a strong fluorescent signal, while ATP could be regenerated for next target recycling. Combing the good fluorescence quenching ability of (+)AuNRs and the Exo Ⅲ assisted signal amplification, a low detection limit of 26 pM was achieved for ATP detection. Notably, the proposed method can be successfully applied for detecting ATP in serum samples, indicating a potential application value in early cancer diagnosis.

A universal aptasensing platform based on cryonase-assisted signal amplification and graphene oxide induced quenching of the fluorescence of labeled nucleic acid probes: application to the detection of theophylline and ATP

This study describes a universal fluorometric method for sensitive detection of analytes by using aptamers. It is based on the use of graphene oxide (GO) and cryonase-assisted signal amplification. GO is a strong quencher of FAM-labeled nucleic acid probes, while cryonase digests all types of nucleic acid probes. This makes the platform widely applicable to analytes for which the corresponding aptamers are available. Theophylline and ATP were chosen as model analytes. In the absence of targets, dye-labeled aptamers are in a flexible single strand state and adsorb on the GO. As a result, the probes are non-fluorescent due to the efficient quenching of dyes by GO. Upon the addition of a specific target, the aptamer/target complex desorbed from the GO surface and the probe becomes fluorescent. The released complex will immediately become a substrate for cryonase digestion and subsequently releasing the target to bind to another aptamer to initiate the next round of cleavage. This cyclic reaction will repeat again and again until all the related-probes are consumed and all fluorophores light up, resulting in significant fluorescent signal amplification. The detection limits are 47 nM for theophylline and 22.5 nM for ATP. This is much better than that of known methods. The assay requires only mix-and-measure steps that can be accomplished rapidly. In our perception, the detection scheme holds great promise for the design enzyme-aided amplification mechanisms for use in bioanalytical methods. Graphical abstract A cryonase-assisted signal amplification (CASA) method has been developed by using graphene oxide (GO) conjugated with a fluorophore-labeled aptamer for fluorescence signal generation. It has a large scope because it may be applied to numerous analytes.

A fluorometric displacement assay for adenosine triphosphate using layered cobalt(II) double hydroxide nanosheets

A turn-on fluorometric method is described for the determination of adenosine-5'-triphosphate (ATP). It is based on the displacement of a dye-labeled oligonucleotide from a cobalt(II) based layered double hydroxide (LDH). Due to the electrostatic and ligand exchange interaction, the FAM-labeled DNA is readily adsorbed on the LDH. This leads to complete and fast quenching of the green fluorescence of the label. However, on addition of ATP, the DNA is detached from the LDH because of the stronger affinity of ATP for LDH. This results in the restoration of the green fluorescence. The effect was used to design a sensitive assay that has a linear response in the 0.5-100 μM ATP concentration range and a 0.23 μM lower detection limit. It was applied to the determination of ATP in spiked serum samples. Graphical abstract Schematic presentation of a fluorometric ATP assay based on the displacement of a dye-labeled oligonucleotide from a layered double hydroxide (LDH).

Doped N/Ag Carbon Dot Catalytic Amplification SERS Strategy for Acetamiprid Coupled Aptamer with 3,3'-Dimethylbiphenyl-4,4'-diamine Oxidizing Reaction

The as-prepared co-doped N/Ag carbon dot (CDNAg) has strong catalysis of H₂O₂ oxidation of 3,3'-dimethylbiphenyl-4,4'-diamine (DBD). It forms an oxidation product (DBDox) with surface-enhanced Raman scattering (SERS) activity at 1605 cm-1 in the silver nanosol substrate, and a CDNAg catalytic amplification with SERS analytical platform can be structured based on aptamer (Apt) with the DBD oxidizing reaction. For example, the aptamer (Apt) of acetamiprid (ACT) can be adsorbed on the surface of CDNAg, resulting in inhibited catalytic activity, the reduced generation of DBDox, and a weakened SERS intensity. When the target molecule ACT was added, it formed a stable Apt-ACT complex and free CDNAg that restored catalytic activity and linearly enhanced the SERS signal. Based on this, we proposed a new quantitative SERS analysis method for the determination of 0.01⁻1.5 μg ACT with a detection limit of 0.006 μg/L.

A colorimetric ATP assay based on the use of a magnesium(II)-dependent DNAzyme

A colorimetric assay for ATP is described that uses a strategy that combines the concept of split Mg(II)-dependent DNAzyme, split aptamer, and hybridization-induced aggregation of gold nanoparticles (AuNPs). Both ATP aptamer and Mg(II)-dependent DNAzyme are split into two fragments which are allocated to two well-designed DNA probes. The probes also possess mutually complementary stem sequences and spacer sequences. In the presence of ATP, the separated DNAzyme sequences in the two probes assemble via the synchronous recognition of ATP with two fragments of the aptamer. Then, the activated DNAzyme catalyzes multiple cycles of the cleavage of its substrate DNA sequence. The latter acts as a linker and induces the aggregation of two types of ssDNA-modified AuNP through the hybridization between the complementary sequences. Thus, the color of the AuNP solution remains red. However, in the absence of ATP, the detached aptamer cannot induce the assembly of DNAzyme to cleave the linker DNA. This results in the aggregation of AuNP and a concomitant color transition from red to purple. This ATP assay, performed at a wavelength of 530 nm, has a linear detection range that extends from 10 pM to 100 nM, with a detection limit of 5.3 pM. It was applied to the detection of ATP in human serum. Conceivably, the strategy has a wide scope in that it may be applied to the colorimetric detection of various other analytes through the split aptamer configuration. Graphical abstract Schematic presentation of colorimetric assay for adenosine triphosphate (ATP) based on the use of a split Mg(II)-dependent DNAzyme, a split aptamer, and by exploiting the hybridization-induced aggregation of gold nanoparticles that leads to a color change from red to purple.

Using N-doped Carbon Dots Prepared Rapidly by Microwave Digestion as Nanoprobes and Nanocatalysts for Fluorescence Determination of Ultratrace Isocarbophos with Label-Free Aptamers

The strongly fluorescent and highly catalytic N-doped carbon dots (CDN) were rapidly prepared by a microwave irradiation procedure and were characterized by electron microscopy (EM), laser scattering, infrared spectroscopy (IR), and by their fluorescence spectrum. It was found that the CDN had a strong catalytic effect on the fluorescence reaction of 3,3',5,5'-tetramethylbenzidine hydroxide ((TMB)⁻H₂O₂) which produced the oxidation product of TMB (TMBOX) with strong fluorescence at 406 nm. The aptamer (Apt) was adsorbed on the CDN surfaces which weakened the fluorescence intensity due to the inhibition of catalytic activity. When the target molecule isocarbophos (IPS) was added, it reacted with the Apt to form a stable conjugate and free CDN which restored the catalytic activity to enhance the fluorescence. Using TMBOX as a fluorescent probe, a highly sensitive nanocatalytic method for determination of 0.025⁻1.5 μg/L IPS was established with a detection limit of 0.015 μg/L. Coupling the CDN fluorescent probe with the Apt⁻IPS reaction, a new CD fluorescence method was established for the simple and rapid determination of 0.25⁻1.5 μg/L IPS with a detection limit of 0.11 μg/L.

Single-Molecule Kinetic Fingerprinting for the Ultrasensitive Detection of Small Molecules with Aptasensors

Aptamers have emerged as promising molecular tools for small-molecule analyte sensing. However, the performance of such aptasensors is generally limited by leakage since it has been difficult to completely suppress signal in the absence of analyte, resulting in a compromise between sensitivity and specificity. Here, we describe a methodology for the ultrasensitive detection of analytes combining aptasensors with single-molecule kinetic fingerprinting. A short, fluorescently labeled DNA probe is utilized to detect the structural changes upon ligand binding to the designed hairpin-shaped aptasensor probe. The Poisson statistics of binding and dissociation events of the DNA probe to single surface-immobilized aptasensor molecules is monitored by total internal reflection fluorescence microscopy, permitting the high-accuracy discrimination of the ligand bound and ligand-free states, resulting in zero background. The programmable dynamics of the hairpin enables fine-tuning of the hybridization kinetics of the fluorescent probe, rendering the acquisition time sufficiently flexible to optimize discrimination. Remarkable detection limits are achieved for a diverse set of analytes when spiked into chicken meat extract: the nucleotide adenosine (0.3 pM), the insecticide acetamiprid (0.35 pM), and the dioxin-like toxin PCB-77 (0.72 pM), which is superior to recently reported aptasensors. Our generalizable method significantly improves the performance of aptasensors, with the potential to extend to other molecular biomarkers.

Detecting transcription factors with allosteric DNA-Silver nanocluster switches

Sensitive and efficient detection of protein markers, such as transcription factors (TFs), is an important issue in postgenomic era. In this paper, we report a DNA nanodevice, allosteric DNA-silver nanocluster switches (AgSwitches), for TFs detection. The mechanism of this nanodevice is based on the binding-induced allostery whereby the binding between AgSwitches and TFs alters the conformation of AgSwitches. This alteration brings DNA-silver nanocluster (DNA-AgNCs) and guanine-rich enhancer sequences (GRS) into close proximity, generating fluorescent enhancement for quantifications. Our results revealed that the sequence design of AgSwitches can be rationally optimized according to stimulated free energy, and we demonstrated that this method can not only be used for detecting TFs in nuclear extracts of cells, but also be developed as a tool for screening inhibitors of TFs. Overall, this work expanded the category allosteric DNA nanodevices by first introducing DNA-AgNCs into this area, and the obtained method was efficient for TFs-related investigations.

A Label-Free Fluorescent AND Logic Gate Aptasensor for Sensitive ATP Detection

In this study, a label-free fluorescent, enzyme-free, simple, highly sensitive AND logic gate aptasensor was developed for the detection of adenosine triphosphate (ATP). Double-stranded deoxyribonucleic acid (DNA) with cohesive ends was attached to graphene oxide (GO) to form an aptasensor probe. ATP and single-stranded DNA were used as input signals. Fluorescence intensity of PicoGreen dye was used as an output signal. The biosensor-related performances, including the logic gate construction, reaction time, linearity, sensitivity, and specificity, were investigated and the results showed that an AND logic gate was successfully constructed. The ATP detection range was found to be 20 to 400 nM (R² = 0.9943) with limit of detection (LOD) of 142.6 pM, and the sensitivity range was 1.846 × 10⁶ to 2.988 × 10⁶ M^-1. This method for the detection of ATP has the characteristics of being simple, low cost, and highly sensitive.