Blank peak current-suppressed electrochemical aptameric sensing platform for highly sensitive signal-on detection of small molecule

A fluorescent probe based on aptamer gold nanoclusters for rapid detection of mercury ions

The mercuric ion (Hg2+) is a hazardous pollutant that is widely distributed in living organisms, foods, and environments with highly toxic and bio-accumulative properties. In the present study, a fluorescent probe based on aptamer gold nanoclusters (apt-AuNCs) was prepared for the ultrasensitive detection of Hg2+ in food. The principle underlying the prepared probe was the quenching of the fluorescence of apt-AuNCs in the presence of Hg2+ due to the strong metallophilic interactions between the 5d10 centers of Hg2+ and Au+. Under optimal conditions, the proposed fluorescent probe exhibited a linear relationship with Hg2+ concentration within the range of 2-200 nM (R2 = 0.9960). In addition, the limit of detection (LOD) was 0.0158 nM, which is below the Chinese standard value of 25 nM for Hg2+ in food. Furthermore, the apt-AuNCs were applied to detect Hg2+ in spinach and crawfish samples, with recovery percentages of 91.99%∼108.06%, meaning that apt-AuNCs could be used as a promising probe to detect Hg2+ in complex food samples.

Finding the Lost Dissociation Constant of Electrochemical Aptamer-Based Biosensors

Electrochemical aptamer-based (E-AB) biosensors afford real-time measurements of the concentrations of molecules directly in complex matrices and in the body, offering alternative strategies to develop innovative personalized medicine tools. While different electroanalytical techniques have been used to interrogate E-AB sensors (i.e., cyclic voltammetry, electrochemical impedance spectroscopy, and chronoamperometry) to resolve the change in electron transfer of the aptamer's covalently attached redox reporter, square-wave voltammetry remains a widely used technique due to its ability to maximize the redox reporter's faradic contribution to the measured current. Several E-AB sensors interrogated with this technique, however, show lower aptamer affinity (i.e., μM-mM) even in the face of employing aptamers that have high affinities (i.e., nM-μM) when characterized using solution techniques such as isothermal titration calorimetry (ITC) or fluorescence spectroscopy. Given past reports showing that E-AB sensor's response is dependent on square-wave interrogation parameters (i.e., frequency and amplitude), we hypothesized that the difference in dissociation constants measured with solution techniques stemmed from the electrochemical interrogation technique itself. In response, we decided to compare six dissociation constants of aptamers when characterized in solution with ITC and when interrogated on electrodes with electrochemical impedance spectroscopy, a technique able to, in contrast to square-wave voltammetry, deconvolute and quantify E-AB sensors' contributions to the measured current. In doing so, we found that we were able to measure dissociation constants that were either separated by 2-3-fold or within experimental errors. These results are in contrast with square-wave voltammetry-measured dissociation constants that are at the most separated by 2-3 orders of magnitude from ones measured by ITC. We thus envision that the versatility and time scales covered by electrochemical impedance spectroscopy offer the highest sensitivity to measure target binding in electrochemical biosensors relying on changes in electron-transfer rates.

Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids

Electrochemical, aptamer-based (E-AB) sensors support continuous, real-time measurements of specific molecular targets in complex fluids such as undiluted serum. They achieve these measurements by using redox-reporter-modified, electrode-attached aptamers that undergo target binding-induced conformational changes which, in turn, change electron transfer between the reporter and the sensor surface. Traditionally, E-AB sensors are interrogated via pulse voltammetry to monitor binding-induced changes in transfer kinetics. While these pulse techniques are sensitive to changes in electron transfer, they also respond to progressive changes in the sensor surface driven by biofouling or monolayer desorption and, consequently, present a significant drift. Moreover, we have empirically observed that differential voltage pulsing can accelerate monolayer desorption from the sensor surface, presumably via field-induced actuation of aptamers. Here, in contrast, we demonstrate the potential advantages of employing cyclic voltammetry to measure electron-transfer changes directly. In our approach, the target concentration is reported via changes in the peak-to-peak separation, ΔE_P, of cyclic voltammograms. Because the magnitude of ΔE_P is insensitive to variations in the number of aptamer probes on the electrode, ΔE_P-interrogated E-AB sensors are resistant to drift and show decreased batch-to-batch and day-to-day variability in sensor performance. Moreover, ΔE_P-based measurements can also be performed in a few hundred milliseconds and are, thus, competitive with other subsecond interrogation strategies such as chronoamperometry but with the added benefit of retaining sensor capacitance information that can report on monolayer stability over time.

Sensing of mercury ions in Porphyra by Copper @ Gold nanoclusters based ratiometric fluorescent aptasensor

A novel aptamer-modified Copper @ Gold nanoclusters (apt-Cu@Au NCs) based ratiometric fluorescent probe was developed for mercury ions (Hg²⁺) determination in Porphyra. The apt-Cu@Au NCs were well dispersed in solution without Hg²⁺ but combined together for the formation of thymidine-Hg-thymidine structure with the addition of Hg²⁺, which further caused the changes in their fluorescence intensities owing to fluorescence resonance energy transfer. Along with that, the changes in fluorescent colors are visible to the naked eye. Accordingly, Hg²⁺ were determined ranging from 0.1 to 9.0 μM by fluorescence analysis with the detection limit of 4.92 nM. Moreover, a homemade device utilizing smartphone and microfluidic chip was designed for colorimetric determination of Hg²⁺ ranging from 0.5 to 7.0 μM with good portability and usefulness. The proposed methods were used for Hg²⁺ detection in Porphyra with the recoveries of 101.83-114.00%, suggesting the considerable potential for evaluating Hg²⁺ levels in aquatic products.

New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection

The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry. The thermodynamic parameters of binding are presented, and its biochemical implications are discussed. The number of binding sites can also be increased, and up to four sites are introduced in a single DNA sequence. Finally, the different sequences are made into fluorescent biosensors based on the structure-switching signaling aptamer design. The one-site aptamer has 3.8-fold higher sensitivity at lower adenosine concentration with a limit of detection of 9.1 μM adenosine, but weaker fluorescence signal at higher adenosine concentrations, consistent with a moderate cooperativity in the original aptamer. This work has offered insights into a classic aptamer for the relationship between the number of binding sites and sensitivity, and a shorter aptamer for improved biosensor design.

A signal-on electrochemical DNA biosensor based on potential-assisted Cu(I)-catalyzed azide-alkyne cycloaddition mediated labeling of hairpin-like oligonucleotide with electroactive probe

A novel electrochemical biosensor was developed for the signal-on detection of sequence-specific DNA by exploiting potential-assisted Cu(I)-catalyzed azide-alkyne cycloaddition (φCuAAC) as an efficient approach for the labeling of hairpin-like oligonucleotide (hairpin) with electroactive probe. The hairpins, dually labeled with thiol and azide at either terminal, were firstly self-assembled on gold electrode and served as the capture probes for the specific recognition of target DNA. Upon hybridization with target DNA, the surface-confined hairpins were unfolded, liberating the azide-containing terminals away from electrode surface. Subsequently, the unfolded hairpins were conveniently and efficiently labeled with ethynylferrocene (EFC) via the φCuAAC. The quantitatively labeled EFC was finally measured via differential pulse voltammetry (DPV) for the signal-on electrochemical detection of sequence-specific DNA. The biosensor presented a good linear response over the range from 1pM to 1nM with a detection limit of 0.62pM. Results also revealed that it was highly specific and held a good detection capability in serum samples. Furthermore, the ability to chemoselectively label hairpin-like oligonucleotide with signal reporter by electrical addressing, together with the simplicity and efficiency of the φCuAAC, makes it compatible with microfluidic devices and microelectrode arrays to achieve the miniaturized and multiplexed detections.

Nanoprobe-Enhanced, Split Aptamer-Based Electrochemical Sandwich Assay for Ultrasensitive Detection of Small Molecules

It is quite challenging to improve the binding affinity of antismall molecule aptamers. We report that the binding affinity of anticocaine split aptamer pairs improved by up to 66-fold by gold nanoparticles (AuNP)-attached aptamers due to the substantially increased local concentration of aptamers and multiple and simultaneous ligand interactions. The significantly improved binding affinity enables the detection of small molecule targets with unprecedented sensitivity, as demonstrated in nanoprobe-enhanced split aptamer-based electrochemical sandwich assays (NE-SAESA). NE-SAESA replaces the traditional molecular reporter probe with AuNPs conjugated to multiple reporter probes. The increased binding affinity allowed us to use 1,000-fold lower reporter probe concentrations relative to those employed in SAESA. We show that the near-elimination of background in NE-SAESA effectively improves assay sensitivity by ∼1,000-100,000-fold for ATP and cocaine detection, relative to equivalent SAESA. With the ongoing development of new strategies for the selection of aptamers, we anticipate that our sensor platform should offer a generalizable approach for the high-sensitivity detection of diverse targets. More importantly, we believe that NE-SAESA represents a novel strategy to improve the binding affinity between a small molecule and its aptamer and potentially can be extended to other detection platforms.

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

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

Enzyme-free surface plasmon resonance aptasensor for amplified detection of adenosine via target-triggering strand displacement cycle and Au nanoparticles

Herein, we combine the advantage of aptamer technique with the amplifying effect of an enzyme-free signal-amplification and Au nanoparticles (NPs) to design a sensitive surface plasmon resonance (SPR) aptasensor for detecting small molecules. This detection system consists of aptamer, detection probe (c-DNA1) partially hybridizing to the aptamer strand, Au NPs-linked hairpin DNA (Au-H-DNA1), and thiolated hairpin DNA (H-DNA2) previously immobilized on SPR gold chip. In the absence of target, the H-DNA1 possessing hairpin structure cannot hybridize with H-DNA2 and thereby Au NPs will not be captured on the SPR gold chip surface. Upon addition of target, the detection probe c-DNA1 is forced to dissociate from the c-DNA1/aptamer duplex by the specific recognition of the target to its aptamer. The released c-DNA1 hybridizes with Au-H-DNA1 and opens the hairpin structure, which accelerate the hybridization between Au-H-DNA1 and H-DNA2, leading to the displacement of the c-DNA1 through a branch migration process. The released c-DNA1 then hybridizes with another Au-H-DNA1 probe, and the cycle starts anew, resulting in the continuous immobilization of Au-H-DNA1 probes on the SPR chip, generating a significant change of SPR signal due to the electronic coupling interaction between the localized surface plasma of the Au NPs and the surface plasma wave. With the use of adenosine as a proof-of-principle analyte, this sensing platform can detect adenosine specifically with a detection limit as low as 0.21 pM, providing a simple, sensitive and selective protocol for small target molecules detection.

Selective lighting up of epiberberine alkaloid fluorescence by fluorophore-switching aptamer and stoichiometric targeting of human telomeric DNA G-quadruplex multimer

Aptamers, that exist naturally in living cells as functional elements and can switch nonfluorescent natural targets to fluorophores, are very useful in developing highly sensitive and selective biosensors and screening functional agents. This work demonstrates that human telomeric G-quadruplex (HTG) can serve as a potential fluorophore-switching aptamer (FSA) to target a natural isoquinoline alkaloid. We found that, among the G-quadruplexes studied here and the various structurally similar alkaloids including epiberberine (EPI), berberine (BER), palmatine (PAL), jatrorrhizine (JAT), coptisine (COP), worenine (WOR), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT), only the HTG DNA, especially with a 5'-TA-3' residue at the 5' end of the G-quadruplex tetrad (5'-TAG3(TTAG3)3-3', TA[Q]) as the minimal sequence, is the most efficient FSA to selectively light up the EPI fluorescence. Compared to the 5' end flanking sequences, the 3' end flanking sequences of the tetrad contribute significantly less to the recognition of EPI. The binding affinity of EPI to TA[Q] (K(d) = 37 nM) is at least 20 times tighter than those of the other alkaloids. The steady-state absorption, steady-state/time-resolved fluorescence, and NMR studies demonstrate that EPI most likely interact with the 5' end flanking sequence substructure beyond the core [Q] and the G-quadruplex tetrad in a much more specific manner than the other alkaloids. The highly selective and tight binding of EPI with the FSA and significantly enhanced fluorescence suggest the potential development of a selective EPI sensor (detection limit of 10 nM). More importantly, EPI, as the brightest FSA emitter among the alkaloids, can also serve as an efficient conformation probe for HTG DNA and discriminate the DNA G-quadruplex from the RNA counterpart. Furthermore, EPI can bind stoichiometrically to each G-quadruplex unit of long HTG DNA multimer with the most significant fluorescence enhancement, which has not been achieved by the previously reported probes. Our work suggests the potential use of EPI as a bioimaging probe and a therapeutic DNA binder.

Target-triggering multiple-cycle amplification strategy for ultrasensitive detection of adenosine based on surface plasma resonance techniques

An ultrasensitive protocol for surface plasma resonance (SPR) detection of adenosine is designed with the aptamer-based target-triggering cascade multiple cycle amplification, and streptavidin-coated Au-NPs (Au NPs-SA) enhancement to enhance the SPR signals. The cascade amplification process consists of the aptamer-based target-triggering nicking enzyme signaling amplification (T-NESA), the nicking enzyme signaling amplification (NESA) and the hybridization chain reaction (HCR), the entire circle amplification process is triggered by the target recognition of adenosine. Upon recognition of the aptamer to target adenosine, DNA s1 is released from the aptamer and then hybridizes with hairpin DNA (HP1). The DNA s1 can be dissociated from HP1 under the reaction of nicking endonuclease to initiate the next hybridization and cleavage process. Moreover, the products of the upstream cycle (T-NESA) (DNA s2 and s3) could act as the "DNA trigger" of the downstream cycle (NESA and HCR) to generate further signal amplification, resulting in the immobilization of abundant Au NPs-SA on the gold substrate, and thus significant SPR enhancement is achieved due to the electronic coupling interaction between the localized surface plasma of Au NPs and the surface plasma wave. This detection method exhibits excellent specificity and sensitivity toward adenosine with a detection limit of 4 fM. The high sensitivity and specificity make this method a great potential for detecting biomolecules with trace amounts in bioanalysis and clinical biomedicine.

Background eliminated signal-on electrochemical aptasensing platform for highly sensitive detection of protein

Using platelet-derived growth factor B chain dimer (PDGF-BB) as the model target, a background current eliminated electrochemical aptameric sensing platform for highly sensitive and signal-on detection of protein is proposed in this paper. Successful fabrication of the biosensor depends on ingenious design of aptamer probe, which contains the aptamer sequence for PDGF-BB and the recognition sequence for EcoRI endonuclease. In the absence of PDGF-BB, the ferrocene labeled aptamer probe folds into a hairpin structure and forms a recognition site for EcoRI. By treatment with endonuclease, the specific and cleavable double-stranded region is cut off and redox-active ferrocene molecule is removed from the electrode surface, and almost no peak current is observed. When binding with target protein, the designed aptamer probe changes its conformation and dissociates the recognition double strand. The integrated aptamer probe is maintained when exposing to EcoRI endonuclease, resulting in obvious peak current. Therefore, a signal-on and sensitive sensing strategy for PDGF-BB detection is fabricated with eliminated background current. Under the optimized experimental conditions, a wide linear response range of 4 orders of magnitude from 20pgmL(-1) to 200ngmL(-1) is achieved with a detection limit of 10pgmL(-1). Moreover, the present aptameric platform is universal for the analysis of a broad range of target molecules of interest by changing and designing the sequence of aptamer probe.

An electrochemical sensing platform based on local repression of electrolyte diffusion for single-step, reagentless, sensitive detection of a sequence-specific DNA-binding protein

In this paper, we report for the first time an electrochemical biosensor for single-step, reagentless, and picomolar detection of a sequence-specific DNA-binding protein using a double-stranded, electrode-bound DNA probe terminally modified with a redox active label close to the electrode surface. This new methodology is based upon local repression of electrolyte diffusion associated with protein-DNA binding that leads to reduction of the electrochemical response of the label. In the proof-of-concept study, the resulting electrochemical biosensor was quantitatively sensitive to the concentrations of the TATA binding protein (TBP, a model analyte) ranging from 40 pM to 25.4 nM with an estimated detection limit of ∼10.6 pM (∼80 to 400-fold improvement on the detection limit over previous electrochemical analytical systems).

Graphene-mesoporous silica-dispersed palladium nanoparticles-based probe carrier platform for electrocatalytic sensing of telomerase activity at less than single-cell level

Human telomerase is a specialized ribonucleoprotein polymerase and is used as a clinical cancer marker and special target for chemotherapy. Traditional telomerase detection uses "telomerase repeat amplification protocol" (TRAP) assay. However, TRAP is questioned because it requires use of DNA polymerases, which is susceptible to polymerase chain reaction (PCR)-derived artifacts and time-consuming. Here, a novel PCR-free, electrocatalytic assay for signal-amplified detection of telomerase activity using graphene-mesoporous silica-dispersed palladium nanoparticles-based probe carrier platform to improve probe-target recognition is reported. The low background noise is achieved by using DNA site-specific cleavage endonuclease and the detection signal is amplified by using hemoglobin. As a highly efficient electron sink, hemoglobin does not carry out direct reduction at the surface, minimizing false positives. These merits make this assay highly sensitive, achieving the sensitivity comparable to TRAP. The developed electrocatalysis assay is PCR-free, simple in design, and fast in operation, therefore avoiding PCR amplification-related errors, which make it more reliable to evaluate telomerase activity for clinical use.

rhEPO/EPO discrimination with ultrasensitive electrochemical biosensor based on sandwich-type nano-Au/ZnO sol-gel/nano-Au signal amplification

This research established a non-labeled electrochemical biosensor for discrimination of recombinant human erythropoietin (rhEPO) and endogenous erythropoietin (EPO). We prepared a glassy carbon electrode (GCE) modified by a unique sandwich-like nano-Au/ZnO sol-gel/nano-Au compound membrane for signal amplification. The porous sol-gel structure facilitates protein activity maintenance and thermostability. Nano-Au is characterized by a large specific surface area, high surface activity, high absorbability, and good electro-conductivity and biocompatibility. By combining the advantages of both ZnO sol-gel and nano-Au, the amount of erythropoietin receptor (EPOR) increased substantially, and electron transfer of EPOR protein and electrode surface increased accordingly. In the present study, the effects of experimental conditions such as nano-Au electrodeposition time and nano-Au concentration were investigated by cyclic voltammetry, and the process of GCE modification was characterized electrochemically. We successfully developed a new method for electrochemical detection of trace rhEPO/EPO. More importantly, the response current change (ΔI) of the nano-Au/ZnO sol-gel/nano-Au modified GCE increases 3-fold when compared with that of the unmodified electrode and the sensor detection sensitivity increases significantly. In conclusion, this electrochemical biosensor is simple to prepare and allows fast, accurate, and specific detection of trace rhEPO in clinical monitoring and stimulant discrimination.

Sensitive chemiluminescence aptasensor based on exonuclease-assisted recycling amplification

We report herein an exonuclease-assisted aptamer-based target recycling amplification strategy for sensitive and selective chemiluminescence (CL) determination of adenosine. This aptasensor is based on target-induced release of aptamers from capture probes immobilized on the 96-well plate surface, and thus leading to a decreased hybridization with gold nanoparticle-functionalized reporter sequences followed by a CL signal. The introduction of exonuclease III catalyzes the stepwise removal of mononucleotides from 3'-hydroxyl termini of duplex DNAs of aptamers, liberating the adenosine. Therefore, a single copy of target adenosine can lead to the release and digestion of numerous aptamer strands from the 96-well plates and ultimately an enhanced sensitivity is achieved. Experimental results revealed that the exonuclease-assisted recycling strategy enabled the monitoring of adenosine with wide working ranges and low detection limits (LOD: 0.5 nM). This new CL strategy might create a novel technology for the detection of various targets and could find wide applications in the environmental and biomedical fields.

An electrochemical aptasensor for chiral peptide detection using layer-by-layer assembly of polyelectrolyte-methylene blue/polyelectrolyte-graphene multilayer

Here we demonstrate for the first time that by physically adsorbing aptamer onto conductive film assembled via alternate adsorption of graphene/polyelectrolyte and methylene blue/polyelectrolyte, a label-free electrochemical aptasensor with high sensitivity and selectivity for peptide detection is constructed. Graphene multilayer derived from layer-by-layer assembly has played significant roles in this sensing strategy: allowing accumulation of methylene blue, facilitating electron transfer and providing much more adsorption site. As compared to previous electrochemical aptasensors, the current sensor based on graphene multilayer alternated with electroactive molecule layer offers extremely high capability for sensitive detection of target without interference of environmental surrounding. This electroactive probe-confined graphene multilayer confers great flexibility to combine with differential pulse voltammetry (DPV) together. In the presence of target d entiomer of arginine vasopressin (D-VP), the binding of peptide to aptamer block the electron transfer process of MB, leading to decreased current peak of DPV. By this way, this electrochemical aptasensor based on electroactive molecule-intercalated graphene multilayer provide highly sensitive and specific detection of D-VP with the lowest detectable concentration of 1 ng mL(-1) and a wide detection range from 1 to 265 ng mL(-1).