Cascade signal amplification strategy for subattomolar protein detection by rolling circle amplification and quantum dots tagging

Sensitive immunosensor for N-terminal pro-brain natriuretic peptide based on N-(aminobutyl)-N-(ethylisoluminol)-functionalized gold nanodots/multiwalled carbon nanotube electrochemiluminescence nanointerface

A novel electrochemiluminescence (ECL) immunosensor was developed for the determination of N-terminal pro-brain natriuretic peptide (NT-proBNP) by using N-(aminobutyl)-N-(ethylisoluminol) (ABEI)-functionalized gold nanodots/chitosan/multiwalled carbon nanotubes (ABEI/GNDs/chitosan/COOH-MWCNTs) hybrid as nanointerface. First, ABEI/GNDs/chitosan/COOH-MWCNTs hybrid nanomaterials were grafted onto the surface of ITO electrode via the film-forming property of hybrid nanomaterials. The anti-NT-proBNP antibody was connected to the surface of modified electrode by virtue of amide reaction via glutaraldehyde. The obtained sensing platform showed strong and stable ECL signal. When NT-proBNP was captured by its antibody immobilized on the sensing platform via immunoreaction, the ECL intensity decreased. Direct ECL signal changes were used for the determination of NT-proBNP. The present ECL immunosensor demonstrated a quite wide linear range of 0.01-100 pg/mL. The achieved low detection limit of 3.86 fg/mL was about 3 orders of magnitude lower than that obtained with electrochemistry method reported previously. Because of the simple and fast analysis, high sensitivity and selectivity, and stable and reliable response, the present immunosensor has been successfully applied to quantify NT-proBNP in practical plasma samples. The success of the sensor in this work also confirms that ABEI/GNDs/chitosan/COOH-MWCNTs hybrid is an ideal nanointerface to fabricate a sensing platform. Furthermore, the proposed strategy could be applied in the detection of other clinically important biomarkers.

Paper-based electrochemiluminescence origami device for protein detection using assembled cascade DNA-carbon dots nanotags based on rolling circle amplification

In this work, we developed a cascade signal amplification strategy for detection of IgG antigen by combining the rolling circle amplification (RCA) technique with oligonucleotide functionalized carbon dots (CDs), based on a paper-based electrochemiluminescence (ECL) origami device (PECLOD) for the first time. In this PECLOD, three-dimensional (3D) macroporous Au-paper electrode was fabricated and employed as the working electrode for specific and efficient antibodies capture. The RCA product containing tandem-repeat sequences could serve as an excellent template for periodic assembly of CDs, which presented per protein recognition event to numerous CDs tags for ECL readout. Under the optimal conditions, the proposed strategy showed remarkable amplification efficiency, very little nonspecific adsorption with good stability, reproducibility, and accuracy. Using human IgG (H-IgG) as a model protein, the designed strategy was successfully demonstrated for the ultrasensitive detection of protein target. The results revealed that the strategy exhibited a dynamic response to H-IgG range from 1.0 fM to 25 pM with a limit of detection as low as 0.15 fM. Importantly, the methodology can be further extended to the detection of other proteins or biomarkers.

A novel and versatile nanomachine for ultrasensitive and specific detection of microRNAs based on molecular beacon initiated strand displacement amplification coupled with catalytic hairpin assembly with DNAzyme formation

A simple and versatile strategy for ultrasensitive and specific detection of microRNAs based on strand displacement amplification and catalytic hairpin assembly.

A netlike rolling circle nucleic acid amplification technique

An isothermal nucleic acid amplification technique termed as netlike rolling circle amplification is proposed. Dense and uniform network morphology of amplified products is first observed, suggesting the ultrahigh amplification efficiency.

Ultrasensitive electrochemical detection of breast cancer cells based on DNA-rolling-circle-amplification-directed enzyme-catalyzed polymerization

An ultrasensitive cytosensor based on DNA-rolling-circle-amplification-directed enzyme-catalyzed polymerization is demonstrated. As a proof of concept, the cytosensor shows excellent sensitivity for MCF-7 cell detection with a lower detection limit of 12 cells per mL.

Ultrasensitive detection of thrombin using surface plasmon resonance and quartz crystal microbalance sensors by aptamer-based rolling circle amplification and nanoparticle signal enhancement

The surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) aptasensors combined with rolling circle amplification and bio-bar-coded AuNP enhancement have been applied to detect the human α-thrombin for the first time. The assay platform exhibited excellent selectivity and sensitivity with detection limit as low as 0.78 aM.

Amplified fluorescence quenching of lucigenin self-assembled inside silica/chitosan nanoparticles by Cl⁻

Fluorescence sensing of an analyte based on the fluorophore collective effect is a reliable, sensitive sensing approach. Many ultralow targets can be detected on the basis of the high sensitivity and signal amplification of the fluorescence sensing system. However, the complicated synthesis procedures, harsh conditions required to design and control the fluorescence molecular probes and conjugated chain length, and the higher cost of synthesis are still challenges. To address these issues, we developed a simple, rapid, and sensitive collective effect based fluorescence sensing platform. In this sensing platform, the fluorophore unit was self-assembled on the wall of the nanopores of the porous structural silica/chitosan nanoparticles (SCNPs) on the basis of the electrostatic interaction and supermolecular interaction between the fluorophores and SiO(-) groups and chitosan. Since these self-assembled fluorophores are close enough to communicate with each other on the basis of the space confinement effect of the pore size, many fluorophore units could interact with a single analyte and produce an amplified fluorescence sensing ability. Chloride ion, an important anion in biological fluids, and lucigenin, a typical fluorescent dye, were used as a model to confirm the proof-of-concept strategy. Our results showed that, compared to free-state lucigenin in solution, the assembled-state lucigenin in SCNPs presented an about 10-fold increase in its Stern-Volmer constant when the concentration of Cl(-) was lower than 10 mM, and this fluorescence nanosensor was also successfully used to sense the chloride ion in living cells.

An ultrasensitive aptameric sensor for proteins based on hyperbranched rolling circle amplification

A novel fluorescent aptameric sensor for thrombin has been developed by combination of the high amplification efficiency of HRCA and the specific function of aptameric recognition.

Studies on voltammetric determination of cadmium in samples containing native and digested proteins

This work focuses on determination of cadmium ions using anodic stripping voltammetry (ASV) on thin film mercury electrode in conditions corresponding to those obtained after digestion of cadmium-based quantum dots and their conjugates. It presents the impact of selected proteins, including potential receptors and surface blocking agents on the voltammetric determination of cadmium. Experiments regarding elimination of interferences related to proteins presence using sodium dodecyl sulfate (SDS) are also shown. Effect of SDS on selected analytical parameters and simplicity of analyses carried out was investigated in the framework of current studies. The significant differences of influence among tested proteins on ASV cadmium determination, as well as the variability in SDS effectiveness as the antifouling agent were observed and explained. This work is especially important for those, who design new bioassays and biosensors with a use of quantum dots as electrochemical labels, as it shows what problems may arise from presence of native and digested proteins in tested samples.

Exploitation of rolling circle amplification for the construction of large phage-display antibody libraries

Phage display antibody libraries have proven to have a significant role in the discovery of therapeutic antibodies and polypeptides with desired biological and physicochemical properties. Obtaining a large and diverse phage display antibody library, however, is always a challenging task. Various steps of this technique can still undergo optimization in order to obtain an efficient library. In the construction of a single chain fragment variable (scFv) phage display library, the cloning of the scFv fragments into a phagemid vector is of crucial importance. An efficient restriction enzyme digestion of the scFv DNA leads to its proper ligation with the phagemid followed by its successful cloning and expression. Here, we are reporting a different approach to enhance the efficiency of the restriction enzyme digestion step. We have exploited rolling circle amplification (RCA) to produce a long strand of DNA with tandem repeats of scFv sequences, which is found to be highly susceptible to restriction digestion. With this important modification, we are able to construct a large phage display antibody library of naive SJL/J mice. The size of the library is estimated as ~10(8) clones. The number of clones containing a scFv fragment is estimated at 90%. Hence, the present results could considerably aid the utilization of the phage-display technique in order to get an efficiently large antibody library.

Disposable electrochemical aptasensor array by using in situ DNA hybridization inducing silver nanoparticles aggregate for signal amplification

Nanomaterials as tracing tags have been widely used in biosensors with high sensitivity and selectivity. In this work, a signal amplification electrochemical aptamer sensing strategy for the detection of protein was designed by combining the hybridization-inducing aggregate of DNA-functionalized silver nanoparticles (AgNPs) and differential pulse stripping voltammetry (DPSV) detection. The multiprobes containing hybridization DNA and aptamers were anchored onto the silver nanoparticles. The protein assay was prepared through the immobilization of capture aptamer that specifically recognizes platelet-derived growth factor (PDGF-BB) on gold nanoparticles modified screen-printed electrode (SPE) array. After a sandwich-type reaction, two kinds of DNA-modified AgNPs were simultaneously added on the electrode surface for specifically recognizing PDGF-BB and forming the AgNPs aggregate caused by in situ hybridization of DNA. Compared to the signal-labeled tag, the tracing aggregate tags showed a strong electroactivity for signal amplification through stripping detection of silver after preoxidation. By using the hybridization-inducing aggregate as electrochemical readouts, the sensor showed wide linear range and low detection limit. The hybridization-inducing AgNPs aggregate were further used as tracing tags in multiplied proteins assays for PDGF-BB and thrombin by using the SPE array chip as sensing platform. The cross-talk between different aptamer-modified electrodes on the same array was avoided because of the advantage of labeled AgNPs. The array detection was also applied in the logic gate operation. The proposed method described here is ideal for multianalytes determination in clinical diagnostics with good analytical performance.

A universal electrochemical sensing system for small biomolecules using target-mediated sticky ends-based ligation-rolling circle amplification

A novel versatile electrochemical platform for ultrasensitive detection of small biomolecules was developed using ligation-rolling circle amplification (L-RCA) with analyte-mediated sticky ends. In order to achieve DNA cyclization, we designed two ss-DNA probes: the leftpart probe could form a "hairpin" structure by denaturing; the rightpart probe could also form a "hairpin" structure based on analyte-activated conformation change. Then the two probes with the same sticky ends (G-AATTC) could be ligated in the presence of Escherichia coli DNA ligase, forming a circular template for rolling circle amplification (RCA), which could be triggered by adding the primer probe and Phi29 DNA polymerase. Electrochemical impedance spectroscopy (EIS) was employed as the detection method. Overall, the proposed L-RCA-based sensing system not only exhibits excellent analytical characteristics with a detection limit of 320 pM and a linear range of 5 orders of magnitude (1 nM-10 μM), but also provides a universal design idea of L-RCA, which broadens the use of DNA amplification method and holds great promise in ultrasensitive bioassay in the future.

A target-triggered strand displacement reaction cycle: the design and application in adenosine triphosphate sensing

A strand displacement reaction (SDR) system that runs solely on oligonucleotides has been developed for the amplification detection of adenosine triphosphate (ATP). It involves a target-induced SDR and an entropy-driven catalytic cycle of two SDRs with five oligonucleotides, denoted as substrate, fuel, catalyst, C-1, and C-2. Catalyst, released from the ATP aptamer-catalyst duplex by ATP molecule, catalyzes the SDRs to finally form the substrate-fuel duplex. All of the intermediates in the catalytic SDR processes have been identified by polyacrylamide gel electrophoresis (PAGE) analysis. The introduction of ATP into the SDR system will induce the ATP aptamer to form G-quadruplex conformation so as to release catalyst and trigger the SDR cycle. When the substrate and C-2 oligonucleotides were labeled with a carboxyfluorescein (FAM) fluorophore and a 4-([4-(dimethylamino)phenyl]azo)benzoic acid (DABCYL) quencher, this SDR catalytic system exhibited a "turn-on" response for ATP. The condition for detecting ATP, such as Mg²⁺ concentration, has been optimized to afford a detection limit of 20 nM. This work provides an enzyme-free biosensing strategy and has potential application in aptamer-based biosensing.

Tapping the potential of quantum dots for personalized oncology: current status and future perspectives

Cancer is one of the most serious health threats worldwide. Personalized oncology holds potential for future cancer care in clinical practice, where each patient could be delivered individualized medicine on the basis of key biological features of an individual tumor. One of the most urgent problems is to develop novel approaches that incorporate the increasing molecular information into the understanding of cancer biological behaviors for personalized oncology. Quantum dots are a heterogeneous class of engineered fluorescent nanoparticles with unique optical and chemical properties, which make them promising platforms for biomedical applications. With the unique optical properties, the utilization of quantum dot-based nanotechnology has been expanded into a wide variety of attractive biomedical applications for cancer diagnosis, monitoring, pathogenesis, treatment, molecular pathology and heterogeneity in combination with cancer biomarkers. Here, we focus on the clinical application of quantum dot-based nanotechnology in personalized oncology, covering topics on individualized cancer diagnosis and treatment by in vitro and in vivo molecular imaging technologies, and in-depth understanding of the biological behaviors of tumors from a nanotechnology perspective. In addition, the major challenges in translating quantum dot-based nanotechnology into clinical application and promising future directions in personalized oncology are also discussed.

General colorimetric detection of proteins and small molecules based on cyclic enzymatic signal amplification and hairpin aptamer probe

In this work, we developed a simple and general method for highly sensitive detection of proteins and small molecules based on cyclic enzymatic signal amplification (CESA) and hairpin aptamer probe. Our detection system consists of a hairpin aptamer probe, a linker DNA, two sets of DNA-modified AuNPs, and nicking endonuclease (NEase). In the absence of a target, the hairpin aptamer probe and linker DNA can stably coexist in solution. Then, the linker DNA can assemble two sets of DNA-modified AuNPs, inducing the aggregation of AuNPs. However, in the presence of a target, the hairpin structure of aptamer probe is opened upon interaction with the target to form an aptamer probe-target complex. Then, the probe-target complex can hybridize to the linker DNA. Upon formation of the duplex, the NEase recognizes specific nucleotide sequence and cleaves the linker DNA into two fragments. After nicking, the released probe-target complex can hybridize with another intact linker DNA and the cycle starts anew. The cleaved fragments of linker DNA are not able to assemble two sets of DNA-modified AuNPs, thus a red color of separated AuNPs can be observed. Taking advantage of the AuNPs-based sensing technique, we are able to assay the target simply by UV-vis spectroscopy and even by the naked eye. Herein, we can detect the human thrombin with a detection limit of 50 pM and adenosine triphosphate (ATP) with a detection limit of 100 nM by the naked eye. This sensitivity is about 3 orders of magnitude higher than that of traditional AuNPs-based methods without amplification. In addition, this method is general since there is no requirement of the NEase recognition site in the aptamer sequence. Furthermore, we proved that the proposed method is capable of detecting the target in complicated biological samples.

Colorimetric and ultrasensitive bioassay based on a dual-amplification system using aptamer and DNAzyme

Rapid detection of ultralow amount of biomarkers in a biologically complex mixture remains a major challenge. Herein, we report a novel aptamer-based protein detection assay that integrates two signal amplification processes, namely, polymerase-mediated rolling-circle amplification (RCA) and DNA enzyme-catalyzed colorimetric reaction. The target biomarker is captured in a sandwich assay by primary aptamer-functionalized microbeads (MBs) and a secondary aptamer that is connected to a RCA primer/circular template complex. RCA reaction, which amplifies the single biomarker binding events by a factor of hundreds to thousands (the first amplification) produces a long DNA molecule containing multiple DNAzyme units. The peroxidase-like DNAzyme catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (the second amplification), which generates a blue-green colorimetric signal. This new biosensing platform permits the ultrasensitive, label-free, colorimetric detection of biomarker in real time. Using platelet-derived growth factor B-chain (PDGF-BB) as a model system, we demonstrated that our assay can detect a protein marker specifically in a serum-containing medium, at a concentration as low as 0.2 pg/mL in ∼2 h, which rivals traditional assays such as ELISA. We anticipate this simple methodology for biomarker detection can find utility in point-of-care applications.

Cascade signal amplification strategy for the detection of cancer cells by rolling circle amplification and nanoparticles tagging

A cascade signal amplification strategy was proposed for detection of cancer cells at ultralow concentration by combining the rolling circle amplification (RCA) technique with oligonucleotide functionalized nanoparticles (NPs), and anodic stripping voltammetric detection. This flexible biosensing system exhibited high sensitivity and specificity with the detection limits of 10 Ramos cells mL(-1).

Sensitive detection of proteins using assembled cascade fluorescent DNA nanotags based on rolling circle amplification

A novel cascade fluorescence signal amplification strategy based on the rolling circle amplification (RCA)-aided assembly of fluorescent DNA nanotags as fluorescent labels and multiplex binding of the biotin-streptavidin system was proposed for detection of protein target at ultralow concentration. In the strategy, fluorescent DNA nanotags are prepared relying on intercalating dye arrays assembled on nanostructured DNA templates by intercalation between base pairs. The RCA product containing tandem-repeat sequences could serve as an excellent template for periodic assembly of fluorescent DNA nanotags, which were presented per protein recognition event to numerous fluorescent DNA nanotags for assay readout. Both the RCA and the multiplex binding system showed remarkable amplification efficiency, very little nonspecific adsorption, and low background signal. Using human IgG as a model protein, the designed strategy was successfully demonstrated for the ultrasensitive detection of protein target. The results revealed that the strategy exhibited a dynamic response to human IgG over a three-decade concentration range from 1.0 pM to 1.0 fM with a limit of detection as low as 0.9 fM. By comparison with the assay of multiple labeling antibodies with the dye/DNA conjugate, the limit of detection was improved by 4 orders. The designed signal amplification strategy would hold great promise as a powerful tool to be applied for the ultrasensitive detection of target protein in immunoassay.

Ultrasensitive and selective detection of nicotinamide adenine dinucleotide by target-triggered ligation-rolling circle amplification

An ultrasensitive fluorescence assay for nicotinamide adenine dinucleotide (NAD(+)) was developed by target-triggered ligation-rolling circle amplification (L-RCA). This novel approach can detect as low as 1 pM NAD(+), much lower than those of previously reported biosensors, and exhibits high discrimination ability even against 200 times excess of NAD(+) analogs.

Signal amplification using functional nanomaterials for biosensing

Signal amplification based on biofunctional nanomaterials has recently attracted considerable attention due to the need for ultrasensitive bioassays and the trend towards miniaturized assays. The biofunctional nanomaterials can not only produce a synergic effect among catalytic activity, conductivity and biocompatibility to accelerate the signal transduction, but also provide amplified recognition events by high loading of signal tags, leading to a highly sensitive and specific biosensing. Most importantly, nanoscaled materials are in direct contact with the environment, which permits them to act as chemical and biological sensors in single-molecule detection of biomolecules. In this tutorial review, we will focus on recent significant advances in signal amplification strategies combining the cross-disciplines of chemistry, biology, and materials science, and highlight some elegant applications of biofunctional nanomaterials as excellent electronic or optical signal tags in ultrasensitive bioanalysis. The biofunctional nanomaterials-based biosensing opens a series of concepts for basic research and offers new tools for detection of trace amounts of a wide variety of analytes in clinical, environmental, and industrial applications.