Attomolar detection of proteins via cascade strand-displacement amplification and polystyrene nanoparticle enhancement in fluorescence polarization aptasensors

Aptamer-enhanced particle aggregation inhibition assay for simple homogeneous protein detection using DNA aptamer and thermo-responsive magnetic nanoparticles

A simple and sensitive homogeneous protein detection system is required for the early detection of biomarkers. Thermo-responsive magnetic particles (TM) have already been developed to achieve easy bound/free separation at the homogeneous protein detection system, but they are still limited owing to the requirement of secondary antibodies and negatively charged polymers, and it is challenging to control the TM aggregation behavior because of the size of the TM. Therefore, at new method to control TM aggregation behavior that is simple, easy, and highly sensitive is required. In this study, we developed a DNA aptamer-based TM assay as a simple protein detection system without additional secondary molecular recognition elements or negatively charged polymer. In the first attempt, a DNA aptamer was modified on the TM surface, and its aggregation behavior was monitored depending on the target molecule concentration. The TM aggregation rate during the heating process decreased depending on the amount of the DNA aptamer and increased depending on the target protein level. This suggests that the DNA aptamer prevented TM aggregation owing to its negative charge and achieved target protein detection owing to the cancellation of repulsion. Capturable aptamers were used in the TM assay to improve the sensitivity and limit of detection. The designed Capture DNA was modified on the TM surface, and the aptamer was captured in the presence of the target protein through a conformational change. Eventually, Capturable aptamer-based TM assay achieved a sub-nanomolar limit of detection and higher sensitivity than that of our initial investigation. Through this study and the ease of the DNA aptamer design, it was shown that the DNA aptamer-modified TM assay enabled the development of a simple and sensitive homogeneous protein detection system.

Contractile Hairpin DNA-Mediated Dual-Mode Strategy for Simultaneous Quantification of Lactoferrin and Iron Ion by Surface-Enhanced Raman Scattering and Fluorescence Analysis

DNA-mediated self-assembly technology with good sensitivity and affinity ability has been rapidly developed in the field of probe sensing. The efficient and accurate quantification of lactoferrin (Lac) and iron ions (Fe³⁺) in human serum and milk samples by the probe sensing method can provide useful clues for human health and early diagnosis of anemia. In this paper, contractile hairpin DNA-mediated dual-mode probes of Fe₃O₄/Ag-ZIF8/graphitic quantum dot (Fe₃O₄/Ag-ZIF8/GQD) NPs were prepared to realize the simultaneous quantification of Lac by surface-enhanced Raman scattering (SERS) and Fe³⁺ by fluorescence (FL). In the presence of targets, these dual-mode probes would be triggered by the recognition of aptamer and release GQDs to produce FL response. Meanwhile, the complementary DNA began to shrink and form a new hairpin structure on the surface of Fe₃O₄/Ag, which produced hot spots and generated a good SERS response. Thus, the proposed dual-mode analytical strategy possessed excellent selectivity, sensitivity, and accuracy due to the dual-mode switchable signals from "off" to "on" in SERS mode and from "on" to "off" in FL mode. Under the optimized conditions, a good linear range was obtained in the range of 0.5-100.0 μg/L for Lac and 0.01-5.0 μmol/L for Fe³⁺ and with detection limits of 0.14 μg/L and 3.8 nmol/L, respectively. Finally, the contractile hairpin DNA-mediated SERS-FL dual-mode probes were successfully applied in the simultaneous quantification of iron ion and Lac in human serum and milk samples.

An immobilization-free electrochemical aptamer-based assay for zearalenone based on target-triggered dissociation of DNA from polydopamine nanospheres with strand displacement amplification

Zearalenone (ZEN), a widespread mycotoxin, can cause great harm to people's health. In order to assay ZEN, an immobilization-free electrochemical sensor has been developed. A multifunctional hairpin DNA has been carefully designed, including three functions: the aptamer for zearalenone (ZEN), primer, and template sequence. This hairpin DNA can anchor on polydopamine nanospheres (PDANSs), which can protect DNA against the digestion of enzymes and prevent the occurrence of strand displacement amplification (SDA). In the presence of ZEN, the hairpin DNA is dissociated from PDANSs due to the interaction between ZEN and the aptamer, and the SDA reaction is initiated with the help of endonuclease and polymerase. During the SDA process, substantial amounts of negatively charged dsDNA are generated. The MB molecules are embedded into the dsDNA grooves to obtain the complex with a negative charge. The confined MB is repelled on the surface of the negatively charged ITO electrode, leading to the decline of the current. This immobilization-free method possesses high sensitivity (LOD of 0.18 pg mL^-1) and good selectivity and can be applied to assay ZEN in corn flour.

Nanomaterials Used in Fluorescence Polarization Based Biosensors

Fluorescence polarization (FP) has been applied in detecting chemicals and biomolecules for early-stage diagnosis, food safety analyses, and environmental monitoring. Compared to organic dyes, inorganic nanomaterials such as quantum dots have special fluorescence properties that can enhance the photostability of FP-based biosensing. In addition, nanomaterials, such as metallic nanoparticles, can be used as signal amplifiers to increase fluorescence polarization. In this review paper, different types of nanomaterials used in in FP-based biosensors have been reviewed. The role of each type of nanomaterial, acting as a fluorescent element and/or the signal amplifier, has been discussed. In addition, the advantages of FP-based biosensing systems have been discussed and compared with other fluorescence-based techniques. The integration of nanomaterials and FP techniques allows biosensors to quickly detect analytes in a sensitive and cost-effective manner and positively impact a variety of different fields including early-stage diagnoses.

Recent advances in fluorescence anisotropy/polarization signal amplification

Fluorescence anisotropy/polarization is an attractive and versatile technique based on molecular rotation in biochemical/biophysical systems. Traditional fluorescence anisotropy/polarization assays showed relatively low sensitivity for molecule detection, because widespread molecular masses are too small to produce detectable changes in fluorescence anisotropy/polarization value. In this review, we discuss in detail how the potential of fluorescence anisotropy/polarization signal approach considerably expanded through the implementation of mass amplification, recycle the target amplification, fluorescence probes structure-switching amplification, resonance energy transfer amplification, and provide perspectives at future directions and applications.

Framework nucleic acid-wrapped protein-inorganic hybrid nanoflowers with three-stage amplified fluorescence polarization for terminal deoxynucleotidyl transferase activity biosensing

Herein, we proposed a terminal deoxynucleotidyl transferase (TdT), a potential biomarker of lymphoid tumors, responsive fluorescence polarization (FP)- sensing protocol based on framework nucleic acid (FNA)-wrapped protein-inorganic hybrid nanoflowers. To achieve this goal, a pair of poly-A-composed extension primers (EPa and EPb) was designed, and protein-inorganic hybrid nanoflowers were synthesized by a biomineralization reaction. EPa was labeled with carboxyfluorescein (FAM) fluorophore to create the preliminary FP signal. EPb was labeled with biotin to conjugate with hybrid nanoflowers. Upon introduction of TdT into the dTTP pool, both EPa and EPb can be catalyzed by TdT to incorporate numerous T bases, thereby facilitating intermolecular hybridization between 'A' and 'T' bases. The final assembled FNA-wrapped hybrid nanoflowers with greatly enhanced molecular volume and weight restrict the free rotation of attached FAMs, causing a great FP enhancement from a designated three-stage FP amplification. Under optimized conditions, the TdT can be detected with a detection limit of 0.023 U/mL and a linear detection from 0.1 U/mL to 100 U/mL within 20 min. As a proof-of-concept study, the first exploitation of FNA and protein-inorganic nanoflowers to improve the FP signal and the merit of FP without sample separation and washing opens a new avenue for biochemical study and disease diagnosis.

Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms

Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10^-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.

A near-infrared-II fluorescence anisotropy strategy for separation-free detection of adenosine triphosphate in complex media

Fluorescence anisotropy (FA) has been widely applied for detecting and monitoring special targets in life sciences. However, matrix autofluorescence restricted its further application in complex biological samples. Herein, we report a near-infrared-II (NIR-II) FA strategy for detecting adenosine triphosphate (ATP) in human serum samples and breast cancer cell lysate, which employed NIR-II fluorescent Ag₂Se quantum dots (QDs) as tags to reduce matrix autofluorescence effect and applied graphene oxide (GO) to enhance fluorescence anisotropy signals. In the presence of ATP, the recognition between NIR-II Ag₂Se QDs labeled aptamer (QD-pDNA) and ATP led to the release of QD-pDNA from GO, resulting in the obvious decrease of FA values. ATP could be quantitatively detected in concentrations ranged from 3 nM to 2500 nM, with a detection limit down to 1.01 nM. This study showed that the developed NIR-II FA strategy could be applied for detecting targets in complex biological samples and had great potential for monitoring interactions between biomolecules in biomedical research.

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.

Functional nucleic acid-based fluorescence polarization/anisotropy biosensors for detection of biomarkers

The sensitive and selective detection of biomarkers plays a crucial role in disease diagnostics, drug discovery, and early screening of cancers. The achievement of this goal highly depends on the continuous development of biosensing technologies. Among them, fluorescence anisotropy/polarization (FA/FP) analysis receives increasing interest due to the advantage of simple operation, fast response, and no background interference. In recent decades, great progress has been achieved in FA/FP sensors thanks to the development of functional nucleic acids (FNAs) including aptamers and nucleic acid enzymes. This review focuses on FNA-based FA/FP sensors for the quantitative detection of biomarkers, such as nucleic acid, small molecules, and proteins. The design strategies, recognition elements, and practical applications are fully highlighted. The article also discusses the challenges of applying FNA-based FA/FP sensors in the next generation and the potential solutions along with future prospects. Graphical abstract.

Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review

Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.

Cascaded multiple recycling amplifications for aptamer-based ultrasensitive fluorescence detection of protein biomarkers

Highly sensitive detection of molecular biomarkers plays a significant role in diagnosing various types of diseases at the early stage. We demonstrated in this paper an ultrasensitive aptamer-based fluorescence method for detecting mucin 1 (MUC1) in human serum via a cascaded multiple recycling signal amplification strategy. The MUC1 target molecules present in the samples cause structure switching of the hairpin aptamer probes, which initiates three cascaded recycling cycles for the cleavage of the fluorescently quenched signal probes to recover significant fluorescence for highly sensitive detection of MUC1. The developed method has a linear range from 100 fM to 1 nM for MUC1 detection. Besides, owing to the substantial signal amplification by the integrated and cascaded recycling cycles, a low detection limit of 35 fM is achieved with high selectivity. Moreover, the monitoring of trace MUC1 in human serum can also be realized with such a method, indicating its great potential for highly sensitive detection of different disease biomarkers.

Colorimetric switchable linker-based bioassay for ultrasensitive detection of prostate-specific antigen as a cancer biomarker

The use of colorimetric bioassays for protein detection is one of the most interesting diagnostic approaches, but their relatively poor detection limits have been a critical issue. In this study, we developed an efficient colorimetric bioassay based on switchable linkers (SLs) for the detection of prostate-specific antigen (PSA), which is one of the most widely used protein biomarkers for the diagnosis of prostate and breast cancers. SLs can cross-link gold nanoparticles (AuNPs) to generate large-scale aggregates and thereby induce precipitation to achieve visual signal amplification. In addition, when SLs are occupied by target proteins (referred to as 'switch-off'), highly sensitive detection is enabled. To maximize sensitivity, we adjusted the total surface area of AuNPs by controlling their concentration. As a result, PSA was detected at an ultralow concentration of 100 fg mL-1. This SL-based assay is shown to be simple, easy to handle and visualize, and highly sensitive. Therefore, in addition to PSA, the proposed SL-based assay could be used to detect other protein biomarkers.

Netlike hybridization chain reaction assembly of DNA nanostructures enables exceptional signal amplification for sensing trace cytokines

The monitoring and detection of molecular biomarkers play crucial roles in disease diagnosis and treatment. In this work, we proposed a target-responsive netlike hybridization chain reaction (nHCR) DNA nanostructure construction method, which can offer an exceptional signal enhancement, for highly sensitive fluorescence detection of cytokine, interferon-gamma (IFN-γ). The presence of the target cytokine can lead to the conformational change of the aptamer recognition hairpin probes and the liberation of the nHCR initiator strands, which further trigger the nHCR process between two dye-labeled and double hairpin-structured probes to form netlike DNA nanostructures. The formation of the DNA nanostructures brings the dyes into close proximity, resulting in significantly amplified fluorescence resonance energy transfer signals for sensitive and enzyme-free detection of IFN-γ. The present method has a detection limit of 1.2 pM and a dynamic linear range of 5 to 1000 pM for IFN-γ detection. Besides, with the high specificity of the aptamer probe and the significant signal amplification of the nHCR, such an IFN-γ detection strategy shows excellent selectivity and high sensitivity, which can be potentially applied to detect IFN-γ in human serums. With such a demonstration of the detection of IFN-γ, this proposed method can be extended for detecting different types of biomolecules.

A T7 exonuclease assisted dual-cycle signal amplification assay of miRNA using nanospheres-enhanced fluorescence polarization

Based on streptavidin coated nanospheres and T7 exonuclease assisted dual-cycle signal amplification, we developed a novel sensitive fluorescence polarization detection method for miRNA. When target miRNA was present in the system, hairpin probe hybridized with miRNA, forming a double-stranded structure. The 5' end of hairpin probe was then recognized and digested by T7 exonuclease, releasing the non-degraded single strand DNA fragments and miRNA. The released target miRNA could trigger the next cycle of hybridization and digestion, releasing more non-degraded fragments from hairpin probe. The fragments could hybridize with a signal probe (with carboxyfluorescein modification at 5'-end and biotin modification at 3'-end). The formed blunt 5'-end of signal probe was then recognized and degraded by T7 exonuclease, releasing the fragments and the fluorophore carboxyfluorescein. The next cycle of hybridization and digestion of signal probe was triggered by the released fragment at the same time. The free carboxyfluorescein cannot connect with streptavidin coated nanospheres which were used as the fluorescence polarization signal amplifier. So, there was a big change of fluorescence polarization signal after adding miRNA into the detection system, due to the different fluorescence polarization signal between nanospheres-captured intact signal probe and free carboxyfluorescein. The detection limit of this method is about 0.001 nM, and it has a good selectivity. In addition, it was also applicable to determine target miRNA in total miRNA extracts and compare the expression level of target miRNA in different cells. Consequently, the proposed method is expected to be used for the potential cancer diagnosis and the related biomedical research.

Miniaturization overcomes macro sample analysis limitations: Salicylate-selective polystyrene nanoparticle-modified optical sensor

Salicylate-selective polystyrene micro-optode is engineered using a mixed solvent method. The size of the particles (200-400 nm) and the distribution of the recognition components onto their surface were elucidated by transmission electron microscope and confocal fluorescence microscope. The polystyrene micro/nanoparticles are modified with thiourea derivative as ionophore, ETH 7075 as chromoionophore, and tridodecylmethyl ammonium chloride (TDMAC) as ion-exchanger. The response mechanism depends on the selective binding of the ionophore at the surface of the particles to salicylate. A concomitant protonation of the chromoionophore results in a decrease in the absorbance at the maximum wavelength, 535 nm. Enabling this sensing interaction at the micro-scale decreases the response time of the optode to be lower than 10 s the concentration range of 3-70 µM, with a detection limit of 2.1 μM. This microsphere sensing platform demonstrated excellent performance in the determination of salicylate in spiked urine samples and in pharmaceutical formulations. Further miniaturization of these micro-optodes promises in-vivo analysis of intracellular analytes.

A fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification and graphene oxide fluorescence quenching for ultrasensitive protein detection

In this work, we have developed a novel fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification (SOIQA) and graphene oxide (GO)-mediated fluorescence quenching for the ultrasensitive detection of proteins in a homogeneous solution. The SOIQA consists of a fluorophore-labeled aptamer hairpin probe containing T7 exonuclease (T7 Exo)-resistant 5'-protruding termini and a mismatch base at its 3'-end, DNA polymerase, T7 Exo and GO. The target analyte binds with the aptamer sequences and unfolds the fluorophore-labeled aptamer hairpin probe to form a new DNA hairpin, inducing the catalytic recycling of the target analyte (assisted by DNA polymerase) and DNA sequences (aided by T7 Exo) to achieve SOIQA, which results in the digestion of numerous fluorophore-labeled aptamer hairpin probes and the generation of a large amount of mononucleotides carrying the fluorophore. These mononucleotide products cannot be adsorbed onto the GO, leading to a dramatic increase in the fluorescence intensity for the amplified detection of the target molecules. In the absence of the target analyte, however, the SOIQA reaction is inhibited and the fluorophore-labeled aptamer hairpin probe is adsorbed onto the GO, leading to an extremely low fluorescence background signal. To test the feasibility of the SOIQA systems, a protein cancer marker, carcinoembryonic antigen (CEA) was used as the model analyte. The developed aptasensor could detect CEA with a detection limit of 28.5 fg mL-1 (∼142 aM), high specificity and a broad detection range of 6 orders of magnitude. And this one-step incubation can be completed in 60 min. In addition, the approach uses only one oligonucleotide strand, and is simple. Moreover, this SOIQA sensing method is suitable for rapid and direct quantification of proteins in complex biological samples such as clinical serum. Considering the simplicity and superior sensitivity/specificity, the developed sensing method provides a promising platform for the analysis of a variety of low-abundance biomolecules.

Gold Nanoparticle Couples with Entropy-Driven Toehold-Mediated DNA Strand Displacement Reaction on Magnetic Beads: Toward Ultrasensitive Energy-Transfer-Based Photoelectrochemical Detection of miRNA-141 in Real Blood Sample

Highly stable circulating microRNAs (miRNAs) are currently recognized as a novel potential biomarker for clinical cancer diagnosis in the early stage. However, limited by its low concentration, high sequence similarity, as well as the numerous interferences in body fluids, detection of miRNA in whole blood with sufficient selectivity and sensitivity is still challenging. Herein, we reported the integration of entropy-driven toehold-mediated DNA strand displacement (ETSD) reaction with magnetic beads (MB) toward the energy-transfer-based photoelectrochemical (PEC) detection of the prostate carcinoma (PCa) biomarker miRNA-141 in a real blood sample. In this protocol, the ETSD reaction was divided into two steps, and cooperated with magnetic separation, target extraction and amplification could be realized in a single test and ultrasensitive detection of miRNA-141 could be achieved in undiluted whole blood sample. This work proposed a new solution for sensitive biomolecular detection in a complex biological milieu and exhibited great promise for future clinical cancer diagnosis.

Magnetic nanoparticles and polydopamine amplified FP aptasensor for the highly sensitive detection of rHuEPO-α

In this paper, an amplified fluorescence polarization (FP) aptasensor based on magnetic nanoparticles @polydopamine (MNP@PDA) was innovatively developed for sensitive detection of recombinant human erythropoietin-alpha(rHuEPO-α). The amplified FP signal was due to the large mass of protein and MNP@PDA. And this assay can be utilized for target separation or recycling based on the magnetic property of MNP@PDA through magnetic separation. Briefly, rHuEPO-α and MNP@PDA were added successively to react with the labeled aptamer (FAM-P1), which both contributed to the increase of FP signal via the formation of FAM-P1-rHuEPO-α and particularly FAM-P1-MNP@PDA complex. The strong interaction between MNP@PDA and FAM-P1 ensured the high efficiency of mass amplification and magnetic separation. As a result, the detection limit for rHuEPO-α was 0.12 pM, 4 orders of magnitude lower than original assay. Besides, three kinds of rHuEPO-α injections, NuPIAO, Epogen and ESPO were used to evaluate the selectivity of this assay in complex matrix with reasonable standard deviation. In a word, this work provides a simple, rapid, non-modified, highly sensitive and selective sensing platform for the detection of rHuEPO-α.

In situ generation of electrochemiluminescent DNA nanoflowers as a signal tag for mucin 1 detection based on a strategy of target and mimic target synchronous cycling amplification

A sensitive electrochemiluminescent (ECL) aptasensor consisting of a novel ECL signal tag of DNA nanoflowers (DNA NFs) and a highly efficient target conversion strategy for the MUC1 assay was developed, which not only increased the stability for luminophore loading, but also greatly improved the detection sensitivity.

A sensitive detection assay based on signal amplification technology for Alzheimer's disease's early biomarker in exosome

Alzheimer's disease (AD) considered as the third health "killer" has seriously threatened the health of the elderly. However, the modern diagnostic strategies of AD present several disadvantages: the low accuracy and specificity resulting in some false-negative diagnoses, and the poor sensitivity leading to a delayed treatment. In view of this situation, a enzyme-free and target-triggered signal amplification strategy, based on graphene oxide (GO) and entropy-driven strand displacement reaction (ESDR) principle, was proposed. In this strategy, when the hairpin structure probes (H)specially binds with beta-amyloid-(1-42) oligomers (Aβ42 oligomers), it's structure will be opened, causing the bases complementary to FAM-labeled replacement probes R (R1 and R2) exposed. At this time, R1 and R2 will hybridize with H, resulting in the bound Aβ42 oligomers released. The released Aβ42 oligomers would participate in the next cycle reaction, making the signal amplified. As a quencher, GO could absorb the free single-stranded DNA R1 and R2 and quench their fluorescence; however, the DNA duplex still exists free and keeps its signal-on. Through the detection of Aβ42 oligomers in exosomes, this ultrasensitive detection method with the advantages of low limit of detection (LOD, 20 pM), great accuracy, excellent precision and convenience provides an excellent prospect for AD's early diagnosis.

Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms

Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.

Ce(III, IV)-MOF electrocatalyst as signal-amplifying tag for sensitive electrochemical aptasensing

Metal-organic frameworks (MOFs) as a new class of porous materials have attracted increasing attention in the field of biomimetic catalysis. This study firstly reports a mixed valence state Ce-MOF possessing intrinsic catalytic activity towards thionine (Thi), and its application in constructing an amplified electrochemical aptasensor for thrombin detection. As noticed, the novel catalytic process combines the advantages of 3D infinite extension of the Ce(III, IV)-MOF skeleton containing large amounts of catalytic sites and spontaneous recycling of the Ce(III)/Ce(IV) for electrochemical reduction of Thi, thereby presenting amplified electrochemical signals. To further improve the aptasensor performance, the high selectivity of proximity binding-induced DNA strand displacement and high efficiency of exonuclease III-assisted recycling amplification were incorporated into the assay. The aptasensor was employed to detect thrombin in complex serum samples, which shows high sensitivity, specificity, stability and reproducibility. This work offers an opportunity to develop MOF-based electrocatalyst as signal-amplifying tag for versatile bioassays and catalytic applications.

Aligner-mediated cleavage of nucleic acids and its application to isothermal exponential amplification

A programmable sequence-specific aligner-mediated cleavage endows strand displacement amplification with excellent universality, high sensitivity, high specificity and simple primer design.

We herein describe a simple and versatile approach to use conventional nicking endonuclease (NEase) for programmable sequence-specific cleavage of DNA, termed aligner-mediated cleavage (AMC), and its application to DNA isothermal exponential amplification (AMC-based strand displacement amplification, AMC-SDA). AMC uses a hairpin-shaped DNA aligner (DA) that contains a recognition site in its stem and two side arms complementary to target DNA. Thus, it enables the loading of an NEase on DA's stem, localization to a specific locus through hybridization of the side arms with target DNA, and cleavage thereof. By using just one NEase, it is easy to make a break at any specific locus and tune the cleavage site to the single-nucleotide scale. This capability also endows the proposed AMC-SDA with excellent universality, since the cleavage of target DNA, followed by a polymerase-catalyzed extension along a particular primer as a key step for initiating SDA, no longer relies on any special sequence. Moreover, this manner of initiation facilitates the adoption of 3′-terminated primers, thus making AMC-SDA highly sensitive and highly specific, as well as simple primer design.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

A label-free colorimetric biosensor for sensitive detection of vascular endothelial growth factor-165

Sensitive detection of a low abundant protein is essential for biomedical research and clinical diagnostics. Herein, we develop a label-free colorimetric biosensor for the sensitive detection of recombinant human vascular endothelial growth factor-165 (VEGF₁₆₅). This biosensor consists of an aptamer-based hairpin probe, an assistant DNA-trigger duplex and a linear template. In the presence of VEGF₁₆₅, the specific binding of VEGF₁₆₅ with the aptamer-based hairpin probe results in the opening of a hairpin probe and the opened hairpin probe subsequently hybridizes with the single-stranded region of the assistant DNA-trigger duplex to initiate the strand displacement amplification (SDA) to yield abundant triggers. The released triggers can further function as the primers to anneal with the hairpin probe and lead to the opening of the hairpin structure, which subsequently hybridizes with the assistant DNA-trigger duplex to initiate the next round of SDA reaction and generates more triggers. Large amounts of triggers could be generated by the synergistic operation of dual SDA reaction, and the obtained triggers can initiate a new round of SDA reaction to yield numerous G-quadruplex DNAzymes, which subsequently catalyze the conversion of ABTS^2- to ABTS˙^- by H₂O₂ to yield a color change with the assistance of a cofactor hemin. In contrast, in the absence of target VEGF₁₆₅, the hairpin probe, the assistant DNA-trigger duplex and the linear template can stably coexist in solution, and thus no color change is observed because no trigger can initiate SDA to generate the G-quadruplex DNAzyme. This biosensor has a low detection limit of 1.70 pM and a dynamic range over 3 orders of magnitude from 24.00 pM to 11.25 nM. Moreover, the biosensor shows excellent specificity toward the target VEGF₁₆₅ and the entire reaction can be carried out in an isothermal manner without the involvement of a high precision thermal cycler, making the current assay extremely cost effective.

A graphene oxide-based strand displacement amplification platform for ricin detection using aptamer as recognition element

The toxic plant protein ricin is a potential agent for criminal or bioterrorist attacks due to the wide availability and relative ease of preparation. Herein, we developed a novel strategy for the detection of ricin B-chain (RTB) based on isothermal strand-displacement polymerase reaction (ISDPR) by using aptamer as a recognition element and graphene oxide (GO) as a low background platform. In this method, ricin-binding aptamer (RBA) hybridized with a short blocker firstly, and then was immobilized on the surface of streptavidin-coated magnetic beads (MBs). The addition of RTB could release the blocker, which could hybridize with the dye-modified hairpin probe and trigger the ISDPR, resulting in high fluorescence intensity. In the absence of RTB, however, the fluorescence of the dye could be quenched strongly by GO, resulting in the extremely low background signal. Thus, RTB could be sensitively detected by the significantly increased fluorescence signal. The linear range of the current analytical system was from 0.75μg/mL to 100μg/mL and the limit of detection (3σ) was 0.6μg/mL. This method has been successfully utilized for the detection of both the RTB and the entire ricin toxin in real samples, and it could be generalized to any kind of target detection based on an appropriate aptamer.

Bivalent Aptasensor Based on Silver-Enhanced Fluorescence Polarization for Rapid Detection of Lactoferrin in Milk

Here we report a novel type of bivalent aptasensor based on silver-enhanced fluorescence polarization (FP) for detection of lactoferrin (Lac) in milk powder with high sensitivity and specificity. The novel two split aptamers were obtained from the aptamer reported in our previous SELEX (systematic evolution of ligands by exponential enrichment) selection, and their minimal structural units were optimized on the basis of their affinity and specificity. Also, dual binding sites of split aptamers were verified. The bivalent aptamers were modified to be linked with signal-molecule fluorescein isothiocyanate (FITC) and enhancer silver decahedral nanoparticles (Ag₁₀NPs). The split aptamers could bind to different sites of Lac and assemble into a split-aptamers-target complex, narrowing the distance between Ag₁₀NPs and FITC dye. As a result, Ag₁₀NPs could produce a mass-augmented and metal-enhanced fluorescence (MEF) effect. In general, ternary amplification based on Ag₁₀NPs, split aptamers, and the MEF effect all contributed to the significant increase of FP values. It was proved that the sensitivity of this assay was about 3 orders of magnitude over traditional aptamer-based homogeneous assays with a detection limit of 1.25 pM. Furthermore, this design was examined by actual milk powder with rapid and high-throughout detection.

Electrochemiluminescence Biosensor Based on 3-D DNA Nanomachine Signal Probe Powered by Protein-Aptamer Binding Complex for Ultrasensitive Mucin 1 Detection

Herein, we fabricated a novel electrochemiluminescence (ECL) biosensor for ultrasensitive detection of mucin 1 (MUC1) based on a three-dimensional (3-D) DNA nanomachine signal probe powered by protein-aptamer binding complex. The assembly of 3-D DNA nanomachine signal probe achieved the cyclic reuse of target protein based on the protein-aptamer binding complex induced catalyzed hairpin assembly (CHA), which overcame the shortcoming of protein conversion with enzyme cleavage or polymerization in the traditional examination of protein. In addition, CoFe₂O₄, a mimic peroxidase, was used as the nanocarrier of the 3-D DNA nanomachine signal probe to catalyze the decomposition of coreactant H₂O₂ to generate numerous reactive hydroxyl radical OH^• as the efficient accelerator of N-(aminobutyl)-N-(ethylisoluminol) (ABEI) ECL reaction to amplify the luminescence signal. Simultaneously, the assembly of 3-D DNA nanomachine signal probe was executed in solution, which led to abundant luminophore ABEI be immobilized around the CoFe₂O₄ surface with amplified ECL signal output since the CHA reaction was occurred unencumberedly in all directions under homogeneous environment. The prepared ECL biosensor showed a favorable linear response for MUC1 detection with a relatively low detection limit of 0.62 fg mL^-1. With excellent sensitivity, the strategy may provide an efficient method for clinical application, especially in trace protein determination.

Label-free colorimetric detection of cancer related gene based on two-step amplification of molecular machine

Highly sensitive detection of K-ras gene is of great significance in biomedical research and clinical diagnosis. Here, we developed a colorimetric biosensing system for the detection of proto-oncogene K-ras based on enhanced amplification effect of DNA molecular machine, where dual isothermal circular strand-displacement amplification (D-SDA) occurs on two arms in one-to-one correspondence. Specifically, we designed a primer-locked hairpin probe (HP) and a primer-contained linear polymerization template (PPT). In the presence of target gene, HP can hybridize with PPT, forming a DNA molecular machine with dual functional arms (called DFA-machine). Each of the two probes in this machine is able to be extended by polymerase on its counterpart species. Moreover, with the help of nicking endonuclease, the dual isothermal polymerization is converted into dual circular strand-displacement amplification, generating a large amount of anti-hemin aptamer-contained products. After binding to hemins, the aptamer/hemin duplex, horseradish peroxidase (HRP)-mimicking DNAzyme, was formed and catalyzed the oxidation of colorless ABTS by H₂O₂, producing a visible green color. The proposed colorimetric assay exhibits a wide linear range from 0.01 to 150nM with a low detection limit of 10pM. More interestingly, the mutations existing in target gene are easily observed by the naked eye. It should be noted that this colorimetric system was proved by the analysis of K-ras gene of SW620 cell lines. The simple and powerful DFA-machine is expected to provide promising potential in the sensitive detection of biomarkers for cancer diagnosis, prognosis and therapy.

A lifetime-sensitive fluorescence anisotropy probe for DNA-based bioassays: The case of SYBR Green

In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer. On the basis of ligand-induced changes in the molar fractions of bound and free forms of SG, the approach provides an unprecedented means for the FA monitoring of the ligand binding to short DNA molecules, allowing the elaboration of a variety of intercalator displacement assays and label-free biosensors that involve diverse DNA structures (duplex, hairpin, G-quadruplex and single-stranded), ligand types (ion, small organic molecule and protein) and binding modes (intercalation, minor groove, allosteric switch). These findings open up promising avenues in the design of a new generation of FA assays.

Target-triggered catalytic hairpin assembly and TdT-catalyzed DNA polymerization for amplified electronic detection of thrombin in human serums

Specific and sensitive detection of protein biomarkers is of great importance in biomedical and bioanalytical applications. In this work, a dual amplified signal enhancement approach based on the integration of catalytic hairpin assembly (CHA) and terminal deoxynucleotidyl transferase (TdT)-mediated in situ DNA polymerization has been developed for highly sensitive and label-free electrochemical detection of thrombin in human serums. The presence of the target thrombin leads to the unfolding and capture of a significant number of hairpin signal probes with free 3'-OH termini on the sensor electrode. Subsequently, TdT can catalyze the elongation of the signal probes and formation of many G-quadruplex sequence replicates with the presence of dGTP and dATP at a molar ratio of 6:4. These G-quadruplex sequences bind hemin and generate drastically amplified current response for sensitive detection of thrombin in a completely label-free fashion. The sensor shows a linear range of 0.5pM-10.0nM and a detection limit of 0.12pM for thrombin. Moreover, the developed sensor can selectively discriminate the target thrombin against other non-target proteins and can be employed to monitor thrombin in human serum samples.

DNA-based hybridization chain reaction and biotin-streptavidin signal amplification for sensitive detection of Escherichia coli O157:H7 through ELISA

This study reported on a novel sandwich enzyme linked immunosorbent assay (ELISA) for the sensitive determination of Escherichia coli O157:H7 (E. coli O157:H7) by using DNA-based hybridization chain reaction (HCR) and biotin-streptavidin signal amplification. The anti-E. coli O157:H7 polyclonal antibody (pAb) was immobilized in the ELISA wells. The anti-E. coli O157:H7 monoclonal antibody (mAb) and initiator strand (DNA1) were labeled on gold nanoparticle (AuNP) to form a mAb-AuNP-DNA1 complex. In the presence of the target E. coli O157:H7, the sandwiched immunocomplex, which is pAb-E. coli O157:H7-mAb-AuNP-DNA1, could be formed. Two types of biotinylated hairpin were subsequently added in the ELISA well. A nicked double-stranded DNA (dsDNA) that contained abundant biotins was formed after HCR. Detection was performed after adding horseradish peroxidase-streptavidin and substrate/chromogen solution. Under optimal conditions, E. coli O157:H7 could be detected in the range of 5×10(2) CFU/mL to 1×10(7) CFU/mL; the limit of detection was 1.08×10(2) CFU/mL in pure culture. The LOD of the novel ELISA was 185 times lower than that of traditional ELISA. The proposed method is considerably specific and can be applied in the detection of whole milk samples inoculated with E. coli O157:H7. The coefficient of variation of in pure culture and in whole milk was 0.99-5.88% and 0.76-5.38%, respectively. This method offers a promising application in the detection of low concentrations of food-borne pathogens.

A TiS2 nanosheet enhanced fluorescence polarization biosensor for ultra-sensitive detection of biomolecules

Development of new strategies for the sensitive and selective detection of ultra-low concentrations of specific cancer markers is of great importance for assessing cancer therapeutics due to its crucial role in early clinical diagnoses and biomedical applications. In this work, we have developed two types of fluorescence polarization (FP) amplification assay strategies for the detection of biomolecules by using TiS2 as a FP enhancer and Zn(2+)-dependent self-hydrolyzing deoxyribozymes as catalysts to realize enzyme-catalyzed target-recycling signal amplification. One approach is based on the terminal protection of small-molecule-linked DNA, in which biomolecular binding to small molecules in DNA-small-molecule chimeras can protect the conjugated DNA from degradation by exonuclease I (Exo I); the other approach is based on the terminal protection of biomolecular bound aptamer DNA, in which biomolecules directly bound to the single strand aptamer DNA can protect the ssDNA from degradation by Exo I. We select folate receptor (FR) and thrombin (Tb) as model analytes to verify the current concept. It is shown that under optimized conditions, our strategies exhibit high sensitivity and selectivity for the quantification of FR and Tb with low detection limits (0.003 ng mL(-1) and 0.01 pM, respectively). Additionally, this strategy is a simple "mix and detect" approach, and does not require any separation steps. This biosensor is also utilized in the analysis of real biological samples, the results agree well with those obtained by the enzyme-linked immunosorbent assay (ELISA).

Recent advances in cytokine detection by immunosensing

The detection of cytokines in body fluids, cells, tissues and organisms continues to attract considerable attention due to the importance of these key cell signaling molecules in biology and medicine. In this review, we describe recent advances in cytokine detection in the course of ongoing pursuit of new analytical approaches for these trace analytes with specific focus on immunosensing. We discuss recent elegant designs of sensing interface with improved performance with respect to sensitivity, selectivity, stability, simplicity, and the absence of sample matrix effects. Various immunosensing approaches based on multifunctional nanomaterials open novel opportunities for ultrasensitive detection of cytokines in body fluids in vitro and in vivo. Methodologies such as suspension arrays also known as bead assays together with optical fiber-based sensors, on their own or in combination with microfluidic devices will continue to have an important role to address the grand challenge of real-time in vivo multiplex cytokine detection.

Novel autonomous protein-encoded aptamer nanomachines and isothermal exponential amplification for ultrasensitive fluorescence polarization sensing of small molecules

We develop a new type of autonomous protein-encoded aptamer nanomachine for amplified fluorescence polarization (FP) sensing of small molecules in homogeneous solutions.

Homogeneous electrochemical detection of ochratoxin A in foodstuff using aptamer-graphene oxide nanosheets and DNase I-based target recycling reaction

A simple and feasible homogeneous electrochemical sensing protocol was developed for the detection of ochratoxin A (OTA) in foodstuff on the immobilization-free aptamer-graphene oxide nanosheets coupling with DNase I-based cycling signal amplification. Thionine-labeled OTA aptamers were attached to the surface of nanosheets because of the strong noncovalent binding of graphene oxide nanosheets with nucleobases and aromatic compounds. The electronic signal was acquired via negatively charged screen-printed carbon electrode (SPCE) toward free thionine molecules. Initially, the formed thionine-aptamer/graphene nanocomposites were suspended in the detection solution and far away from the electrode, thereby resulting in a weak electronic signal. Upon addition of target OTA, the analyte reacted with the aptamer and caused the dissociation of thionine-aptamer from the graphene oxide nanosheets. The newly formed thionine-aptamer/OTA could be readily cleaved by DNase I and released target OTA, which could retrigger thionine-aptamer/graphene nanocomposites with target recycling to generate numerous free thionine molecules. Free thionine molecules were captured by negatively charged SPCE, each of which could produce an electrochemical signal within the applied potentials. Under optimal conditions, graphene-based aptasensing platform could exhibit good electrochemical responses for the detection of OTA at a concentration as low as 5.6pg/mL. The reproducibility, precision and selectivity of the system were acceptable. Importantly, the method accuracy was comparable with commercialized OTA ELISA kit when using for quantitative monitoring of contaminated wheat samples.