Reversible electronic nanoswitch based on DNA G-quadruplex conformation: A platform for single-step, reagentless potassium detection

Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets

Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.

Highly Selective Detection of K+ Based on a Dimerized G-Quadruplex DNAzyme

Potassium ion (K⁺) plays a crucial role in biological systems, such as maintaining cellular processes and causing diseases. However, specifically, the detection of K⁺ is extremely challenging because of the coexistence of the chemically similar ion of Na⁺ under physiological conditions. In this work, a K⁺ specific biosensor is constructed on the basis of a dimerized G-quadruplex (GQ) DNA, which is promoted by K⁺, and the enzymatic activity of the resulting DNAzyme depends on the concentration of the K⁺. The K⁺ in a 1-200 mM concentration range can be selectively detected by visual color, UV-Vis absorbance or fluorescence even if the concentration of the accompanying Na⁺ is up to 140 mM at an ambient condition up to 45 °C. In addition, this system can also be used to selectively detect NH₄⁺ in a 5-200 mM concentration range. This dimerized DNAzyme offers a new type of biosensor with a potential application in the biological system.

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.

Structural requirement of G-quadruplex/aptamer-combined DNA macromolecule serving as efficient drug carrier for cancer-targeted drug delivery

Photodynamic therapy (PDT) as a clinical cancer treatment method has been used to treat carcinomas in different organs, and G-quadruplex-based DNA nanocompartments serving as the carriers of cationic porphyrin photosensitizers, especially combined with cell-targeting aptamers, is considered to offer new opportunities for future cancer treatment. However, the structural features of G-quadruplex/aptamer complexes suitable for the capsulation of photosensitizers and target cell recognition is unexplored so far. In this study, unimolecular (UM), bimolecular (BM) and tetramolecular (TM) G-quadruplex structures were used as the drug loading compartments and grafted onto tumor cell-targeting aptamer Sgc8, constructing several targeting drug delivery vehicles (T-GMVs). Besides the binding affinity of resulting DNA architectures for target cells and cell recognition specificity were explored in a comparative fashion, the drug loading capability and cancer therapy efficacy were evaluated using TMPyP4 as the model porphyrin-based drug. The experimental results show that only TM G-quadruplex structure is suitable to combine with Sgc8 for the development of drug delivery vehicle and the as-prepared T-GMV- TMPyP4 complexes display the desirable cancer therapy efficacy, holding the potential application in the future cancer therapy. More importantly, T-GMV- TMPyP4 is expected to lay the scientific groundwork for the successful development of G-quadruplex-based photosensitizer drug delivery carriers for the targeted cancer therapy.

Challenges in Electrochemical Aptasensors and Current Sensing Architectures Using Flat Gold Surfaces

In recent years, reagentless aptamer biosensors, named aptasensors, have shown significant advancements. Particularly, electrochemical aptasensors could change the field of biosensors in this era, where digitalization seems to be a common goal of many fields. Biomedical devices are integrating electronic technologies for detecting pathogens, biomolecules, small molecules, and ions, and the physical-chemical properties of nucleic acid aptamers makes them very interesting for these devices. Aptamers can be easily synthesized and functionalized with functional groups for immobilization and with redox chemical groups that allow for the conversion of molecular interactions into electrical signals. Furthermore, non-labeled aptamers have also been utilized. This review presents the current challenges involved in aptasensor architectures based on gold electrodes as transducers.

DNA conformational polymorphism for biosensing applications

In this mini review, we will briefly introduce the rapid development of DNA conformational polymorphism in biosensing field, including canonical DNA duplex, triplex, quadruplex, DNA origami, as well as more functionalized DNAs (aptamer, DNAzyme etc.). Various DNA structures are adopted to play important roles in sensor construction, through working as recognition receptor, signal reporter or linking staple for signal motifs, etc. We will mainly summarize their recent developments in DNA-based electrochemical and fluorescent sensors. For the electrochemical sensors, several types will be included, e.g. the amperometric, electrochemical impedance, electrochemiluminescence, as well as field-effect transistor sensors. For the fluorescent sensors, DNA is usually modified with fluorescent molecules or novel nanomaterials as report probes, excepting its core recognition function. Finally, general conclusion and future perspectives will be discussed for further developments.

Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications

Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity. This review discusses the recent advances on the electrochemical characterization, design, and applications of G-quadruplex electrochemical biosensors in the evaluation of metal ions, G-quadruplex ligands, and other small organic molecules, proteins, and cells. The electrochemical and atomic force microscopy characterization of G-quadruplexes is presented. The incubation time and cations concentration dependence in controlling the G-quadruplex folding, stability, and nanostructures formation at carbon electrodes are discussed. Different G-quadruplex electrochemical biosensors design strategies, based on the DNA folding into a G-quadruplex, the use of G-quadruplex aptamers, or the use of hemin/G-quadruplex DNAzymes, are revisited.

Ultrasensitive detection of Ag(I) based on the conformational switching of a multifunctional aptamer probe induced by silver(I)

We for the first time confirmed that the low concentrations of Ag(I) could induce a silver specific aptamer probe (SAP) from a random coil sequence form to G-quadruplex structure. Thereby, a novel highly sensitive fluorescence strategy for silver(I) assay was established. The designed multifunctional SAP could act as a recognition element for Ag(I) and a signal reporter. The use of such a SAP can ultrasensitively and selectively detect Ag(I), giving a detection limit down to 0.64nM. This is much lower than those reported by related literatures. This strategy has been applied successfully for the detection of Ag(I) in real samples, further proving its reliability. Taken together, the designed SAP is not only a useful recognition and signal probe for silver, but also gives a platform to study the interaction of monovalent cations with DNA.

Hi-fidelity discrimination of isomiRs using G-quadruplex gatekeepers

Core microRNA (miRNA) sequences exist as populations of variants called isomiRs made up of different lengths and nucleotide compositions. In particular, the short sequences of miRNA make single-base isomiR mismatches very difficult to be discriminated. Non-specific hybridizations often arise when DNA probe-miRNA target hybridization is the primary, or initial, mode of detection. These errors then become exacerbated through subsequent amplification steps. Here, we present the design of DNA probes modified with poly-guanine (PG) tracts that were induced to form G-quadruplexes (G4) for hi-fidelity discrimination of miRNA core target sequence from single-base mismatched isomiRs. We demonstrate that, when compared to unmodified probes, this G4 'gate-keeping' function within the G4-modified probes enables more stringent hybridization of complementary core miRNA target transcripts while limiting non-specific hybridizations. This increased discriminatory power of the G4-modified probes over unmodified probes is maintained even after further reverse transcriptase extension of probe-target hybrids. Enzymatic extension also enhanced the clarity and sensitivity of readouts and allows different isomiRs to be distinguished from one another via the relative positions of the mismatches.

Ultrasensitive electrochemical biosensor based on the oligonucleotide self-assembled monolayer-mediated immunosensing interface

Highly sensitive and selective quantitation of a variety of proteins over a wide concentration range is highly desirable for increased accuracy of biomarker detection or for multidisease diagnostics. In the present contribution, using human immunoglobulin G (HIgG) as the model target protein, an electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer-mediated (OSAM) sensing interface. For this immunosensor, the "signal-on" signaling mechanism and enzymatic signal amplification effect were integrated into one sensing architecture. Moreover, the thiolated flexible single-stranded DNAs immobilized onto gold electrode surface not only performs the wobbling motion to facilitate the electron transfer between the electrode surface and biosensing layer but also fundamentally prohibiting the direct interaction of proteins with gold substrate. Thus, the electrochemical signal could be efficiently enhanced and the unspecific adsorption or cross-reaction might be eliminated. As a result, utilizing the newly-proposed immunosensor, the HIgG can be detected down to 0.5 ng/mL, and the high detection specificity is offered. The successful design of OSAM and the highly desirable detection capability of new immunosensor are expected to provide a perspective for fabricating new robust immunosensing platform and for promising potential of oligonucleotide probe in biological research and biomedical diagnosis.

Maximizing the Signal Gain of Electrochemical-DNA Sensors

Electrochemical DNA (E-DNA) sensors have emerged as a promising class of biosensors capable of detecting a wide range of molecular analytes (nucleic acids, proteins, small molecules, inorganic ions) without the need for exogenous reagents or wash steps. In these sensors, a binding-induced conformational change in an electrode-bound "probe" (a target-binding nucleic acid or nucleic-acid-peptide chimera) alters the location of an attached redox reporter, leading to a change in electron transfer that is typically monitored using square-wave voltammetry. Because signaling in this class of sensors relies on binding-induced changes in electron transfer rate, the signal gain of such sensors (change in signal upon the addition of saturating target) is dependent on the frequency of the square-wave potential pulse used to interrogate them, with the optimal square-wave frequency depending on the structure of the probe, the nature of the redox reporter, and other features of the sensor. Here, we show that, because it alters the driving force of the redox reaction and thus electron transfer kinetics, signal gain in this class of sensors is also strongly dependent on the amplitude of the square-wave potential pulse. Specifically, we show here that the simultaneous optimization of square-wave frequency and amplitude produces large (often more than 2-fold) increases in the signal gain of a wide range of E-DNA-type sensors.

The aptamer DNA-templated fluorescence silver nanoclusters: ATP detection and preliminary mechanism investigation

Two general and reliable fluorescence sensors were proposed in this work utilizing aptamer DNA-templated silver nanoclusters (Ag NCs). Both DNA-AgNCs could be used for label-free detecting of ATP with the limits of detection of 0.44 and 0.65mM. One of them was further applied to monitor the activity of adenosine deaminase (ADA). In our effort to elucidate the light-up mechanism, we studied a total of six Ag NCs prepared by different DNA sequences, and found that they showed different sensitivity to ATP. Both BT3T3- and BT3T3(R)-templated Ag NCs were chose to make particular studies by UV-vis, TEM, fluorescence, and TCSPC methods. The results showed that when DNA-Ag NCs was kept for 1.5h and presented a strong fluorescence, the addition of ATP failed to cause a large change of fluorescence intensity; on the contrary, after Ag NCs was kept for 24h and emitted a weak fluorescence, adding ATP was able to result in the large fluorescence enhanced of 43 and 33 times for BT3T3- and BT3T3(R)-templated Ag NCs, respectively. The possible mechanism was also suggested that ATP binding to aptamer segment of template induced the change of the DNA secondary structure, which made the aggregated Ag nanoparticles disperse into Ag NCs with an average diameter of about 2nm that were responsible for the large fluorescence increase. Moreover, ATP could protect the fluorescence intensity of BT3T3(R)-templated Ag NCs from quenching for at least 9h.

Electrostatic gating in carbon nanotube aptasensors

Synthetic DNA aptamer receptors could boost the prospects of carbon nanotube (CNT)-based electronic biosensors if signal transduction can be understood and engineered. Here, we report CNT aptasensors for potassium ions that clearly demonstrate aptamer-induced electrostatic gating of electronic conduction. The CNT network devices were fabricated on flexible substrates via a facile solution processing route and non-covalently functionalised with potassium binding aptamers. Monotonic increases in CNT conduction were observed in response to increasing potassium ion concentration, with a level of detection as low as 10 picomolar. The signal was shown to arise from a specific aptamer-target interaction that stabilises a G-quadruplex structure, bringing high negative charge density near the CNT channel. Electrostatic gating is established via the specificity and the sign of the current response, and by observing its suppression when higher ionic strength decreases the Debye length at the CNT-water interface. Sensitivity towards potassium and selectivity against other ions is demonstrated in both resistive mode and real time transistor mode measurements. The effective device architecture presented, along with the identification of clear response signatures, should inform the development of new electronic biosensors using the growing library of aptamer receptors.

Sensitive colorimetric detection of K(I) using catalytically active gold nanoparticles triggered signal amplification

In this work, we report a simple, ultrasensitive, and feasible colorimetric assay for metal ion (K(+), used as a model) via inherent peroxidase-like enzymatic amplification strategy of gold nanoparticles (AuNPs). It is shown that peroxidase-like activity of AuNPs can be improved dramatically by its surface activation with target-specific aptamer molecules. Whereas when the target exists, the aptamers leave the surface of AuNPs in a target concentration-dependent manner, resulting in a decrease of the nanoenzymatic catalytic ability of AuNPs. Thus, K(+) can be quantified in the presence of AuNPs by using a colorimetric sensing probe (3,3',5,5'-tetramethylbenzidine). The color change of the solution is relevant to the dose of the target, and this can be achieved with the naked eyes and monitored by UV-vis spectrometry. A linear dependence between the absorbance and target K(+) concentration is obtained under optimal conditions in the range from 0. 1 nM to 1 μM with a detection limit (LOD) of 0.06 nM estimated at the 3Sblank level. The sensitivity displays to be 2-9 orders of magnitude better than those of other K(+) detection methods. This sensing strategy may in principle be universally applicable for the detection of a range of environmental or biomedical molecules of interest.

Superior fluorescent probe for detection of potassium ion

Here, a simple, and highly sensitive fluorescent assay is designed to monitor K(+). The versatile, robust biosensing strategy is based on the specific recognition utility of label-free aptamers with their targets and PicoGreen dye as the signal probe. The aptamers undergo a conformational change to a secondary structure such as G-quadruplex in the presence of targets. In addition to a conformational change with its targets, the remaining single-stranded DNA (ssDNA) aptamer form a duplex structure with its complete complementary sequence. Conformational changes of aptamers as well as fluorescence amplification produce clear signal-off in the presence of targets. Fluorescent assay employing this mechanism for the detection of K(+) is highly sensitive, and selective. The detection limit of the K(+) assay is determined to be 2.37 pM. The sensing strategy is low-cost and simple in its operation without requirement for complex labeling of probe DNA or sophisticated synthesis of the fluorescent compound. Also, the method has less structural requirement of complexes of aptamers with their targets, thus rending its wilder applications for various targets.

Seven essential questions on G-quadruplexes

The helical duplex architecture of DNA was discovered by Francis Crick and James Watson in 1951 and is well known and understood. However, nucleic acids can also adopt alternative structural conformations that are less familiar, although no less biologically relevant, such as the G-quadruplex. G-quadruplexes continue to be the subject of a rapidly expanding area of research, owing to their significant potential as therapeutic targets and their unique biophysical properties. This review begins by focusing on G-quadruplex structure, elucidating the intermolecular and intramolecular interactions underlying its formation and highlighting several substructural variants. A variety of methods used to characterize these structures are also outlined. The current state of G-quadruplex research is then addressed by proffering seven pertinent questions for discussion. This review concludes with an overview of possible directions for future research trajectories in this exciting and relevant field.

A gold nanoparticle-based label free colorimetric aptasensor for adenosine deaminase detection and inhibition assay

A novel strategy for the fabrication of a colorimetric aptasensor using label free gold nanoparticles (AuNPs) is proposed in this work, and the strategy has been employed for the assay of adenosine deaminase (ADA) activity. The aptasensor consists of adenosine (AD) aptamer, AD and AuNPs. The design of the biosensor takes advantage of the special optical properties of AuNPs and the interaction between AuNPs and single-strand DNA. In the absence of ADA, the AuNPs are aggregated and are blue in color under appropriate salt concentration because of the grid structure of an AD aptamer when binding to AD, while in the presence of the analyte, AuNPs remain dispersed with red color under the same concentration of salt owing to ADA converting AD into inosine which has no affinity with the AD aptamer, thus allowing quantitative investigation of ADA activity. The present strategy is simple, cost-effective, selective and sensitive for ADA with a detection limit of 1.526 U L(-1), which is about one order of magnitude lower than that previously reported. In addition, a very low concentration of the inhibitor erythro-9-(2-hydroxy-3-nonyl) adenine (EHNA) could generate a distinguishable response. Therefore, the AuNP-based colorimetric biosensor has great potential in the diagnosis of ADA-relevant diseases and drug screening.

Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems

This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.

Colorimetric aptasensor using unmodified gold nanoparticles for homogeneous multiplex detection

Colorimetric aptasensors using unmodified gold nanoparticles (AuNPs) have attracted much attention because of their low cost, simplicity, and practicality, and they have been developed for various targets in the past several years. However, previous research has focused on developing single-target assays. Here, we report the development of a homogeneous multiplex aptasensor by using more than one class of aptamers to stabilize AuNPs. Using sulfadimethoxine (SDM), kanamycin (KAN) and adenosine (ADE) as example targets, a KAN aptamer (750 nM), an SDM aptamer (250 nM) and an ADE aptamer (500 nM) were mixed at a 1∶1∶1 volume ratio and adsorbed directly onto the surface of unmodified AuNPs by electrostatic interaction. Upon the addition of any of the three targets, the conformation of the corresponding aptamer changed from a random coil structure to a rigid folded structure, which could not adsorb and stabilize AuNPs. The AuNPs aggregated in a specific reaction buffer (20 mM Tris-HCl containing 20 mM NaCl and 5 mM KCl), which led to a color change from red to purple/blue. These results demonstrate that the multiplex colorimetric aptasensor detected three targets simultaneously while maintaining the same sensitivity as a single-target aptasensor for each individual target. The multiplex aptasensor could be extended to other aptamers for various molecular detection events. Due to its simple design, easy operation, fast response, cost effectiveness and lack of need for sophisticated instrumentation, the proposed strategy provides a powerful tool to examine large numbers of samples to screen for a small number of potentially positive samples containing more than one analyte, which can be further validated using sophisticated instruments.

Toehold strand displacement-driven assembly of G-quadruplex DNA for enzyme-free and non-label sensitive fluorescent detection of thrombin

Based on a new signal amplification strategy by the toehold strand displacement-driven cyclic assembly of G-quadruplex DNA, the development of an enzyme-free and non-label aptamer sensing approach for sensitive fluorescent detection of thrombin is described. The target thrombin associates with the corresponding aptamer of the partial dsDNA probes and liberates single stranded initiation sequences, which trigger the toehold strand displacement assembly of two G-quadruplex containing hairpin DNAs. This toehold strand displacement reaction leads to the cyclic reuse of the initiation sequences and the production of DNA assemblies with numerous G-quadruplex structures. The fluorescent dye, N-Methyl mesoporphyrin IX, binds to these G-quadruplex structures and generates significantly amplified fluorescent signals to achieve highly sensitive detection of thrombin down to 5 pM. Besides, this method shows high selectivity towards the target thrombin against other control proteins. The developed thrombin sensing method herein avoids the modification of the probes and the involvement of any enzyme or nanomaterial labels for signal amplification. With the successful demonstration for thrombin detection, our approach can be easily adopted to monitor other target molecules in a simple, low-cost, sensitive and selective way by choosing appropriate aptamer/ligand pairs.

Bio-nanogate controlled enzymatic reaction for virus sensing

The objective of this study was to develop an aptamer-based bifunctional bio-nanogate, which could selectively respond to target molecules, and control enzymatic reaction for electrochemical measurements. It was successfully applied for sensitive, selective, rapid, quantitative, and label-free detection of avian influenza viruses (AIV) H5N1. A nanoporous gold film with pore size of ~20 nm was prepared by a metallic corrosion method, and the purity was checked by energy-dispersive X-ray spectroscopy (EDS) study. To improve the performance of the bio-nanogate biosensor, its main analytical parameters were studied and optimized. We demonstrated that the developed bio-nanogate was capable of controlling enzymatic reaction for AIV H5N1 sensing within 1h with a detection limit of 2(-9)HAU (hemagglutination units). The enzymatic reaction was able to cause significant current change due to the presence of target AIV. A linear relationship was found in the virus titer range of 2(-10)-2(2)HAU. No interference was observed from non-target AIV subtypes such as H1N1, H2N2, H4N8 and H7N2. The developed approach could be adopted for sensing of other viruses.

DNA as sensors and imaging agents for metal ions

Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.

Colorimetric detection of potassium ions using aptamer-functionalized gold nanoparticles

Herein, a simple and novel colorimetric method for detection of potassium ions (K(+)) was developed. The colorimetric experiments revealed that upon the addition of K(+), the conformation of anti-K(+) aptamer in solution changed from random coil structure to compact rigid G-quadruplex one. This compact rigid G-quadruplex structure could not protect AuNPs against K(+)-induced aggregation, and thus the visible color change from wine-red to blue-purple could be observed by the naked eye. The linear range of the colorimetric aptasensor covered a large variation of K(+) concentration from 5 nM to 1 μM and the detection limit of 5 nM was obtained. Moreover, this assay was able to detect K(+) with high selectivity and had great potential applications.

Aptamer biosensor for label-free impedance spectroscopy detection of potassium ion based on DNA G-quadruplex conformation

Herein, a label-free and highly sensitive electrochemical impedance spectroscopy (EIS) aptasensor for the detection of potassium ion (K⁺) was developed based on a conformational change in which a K⁺-stabilized single stranded DNA (ssDNA) with G-rich sequence was used as the recognition element. In the measurement of K⁺ ions, the change in interfacial electron transfer resistance (R(ct)) of the sensor using a redox couple of [Fe(CN)₆]³⁻/⁴⁻ as the probe was monitored. In the presence of K⁺, the G-rich DNA folded into the G-quadruplex structure, and then K⁺ can bind to the G-quadruplex structure, leading to an increase in the R(ct). The Rct increased with K⁺ concentration, and the plot of R(ct) against the logarithm of K⁺ concentration is linear over the range from 0.1 nM to 1 mM with a detection limit of 0.1 nM. Other metal ions, such as Ca²⁺, Mg²⁺, Na⁺, Li⁺, Al³⁺, Zn²⁺, Cu²⁺, and Ni²⁺ caused no notable interference on the detection of K⁺. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.

Quantification of the Na+/K+ ratio based on the different response of a newly identified G-quadruplex to Na+ and K+

A G-quadruplex is identified which can exhibit two different motifs, respectively, corresponding to Na(+) and K(+). The relative amount of each motif is related to the Na(+)/K(+) ratio. Based on selective recognition of the G-quadruplex motifs by a cyanine dye aggregate, a method for both colorimetric and quantitative measurements of Na(+)/K(+) ratios is constructed.

A universal and label-free aptasensor for fluorescent detection of ATP and thrombin based on SYBR Green I dye

A facile and universal aptamer-based label-free approach for selective and sensitive fluorescence detection of proteins and small biomolecules by using the SYBR Green I (SGI) dye is developed. This robust versatile biosensing strategy relies on fluorescence turn-off changes of SGI, resulting from target-induced structure switching of aptamers. Upon binding with the targets, the aptamers dissociate from the respective cDNA/aptamer duplexes, leading to the release of the dsDNA-intercalated SGI into solution and the quenching of the corresponding fluorescence intensities. Such target-induced conformational changes and release of aptamers from the DNA duplexes essentially lead to the change in the fluorescence signal of the SGI and thus constitute the mechanism of our aptamer-based label-free fluorescence biosensor for specific target analyses. Under optimized conditions, our method exhibits high sensitivity and selectivity for the quantification of ATP and thrombin with low detection limits (23.4 nM and 1.1 nM, respectively). Compared with previous reported methods for aptamer-based detection of ATP and thrombin, this label-free approach is selective, simple, convenient and cost-efficient without any chemical labeling of the probe or the target. Therefore, the present strategy could be easily applicable to biosensors that target a wide range of biomolecules.

An electronic channel switching-based aptasensor for ultrasensitive protein detection

Due to the ubiquity and essential of the proteins in all living organisms, the identification and quantification of disease-specific proteins are particularly important. Because the conformational change of aptamer upon its target or probe/target/probe sandwich often is the primary prerequisite for the design of an electrochemical aptameric assay system, it is extremely difficult to construct the electrochemical aptasensor for protein assay because the corresponding aptamers cannot often meet the requirement. To circumvent the obstacles mentioned, an electronic channel switching-based (ECS) aptasensor for ultrasensitive protein detection is developed. The essential achievement made is that an innovative sensing concept is proposed: the hairpin structure of aptamer is designed to pull electroactive species toward electrode surface and makes the surface-immobilized IgE serve as a barrier that separates enzyme from its substrate. It seemingly ensures that the ECS aptasensor exhibits most excellent assay features, such as, a detection limit of 4.44×10(-6)μg mL(-1) (22.7fM, 220zmol in 10-μL sample) (demonstrating a 5 orders of magnitude improvement in detection sensitivity compared with classical electronic aptasensors) and dynamic response range from 4.44×10(-6) to 4.44×10(-1)μg mL(-1). We believe that the described sensing concept here might open a new avenue for the detection of proteins and other biomacromolecules.

Aptamer-based highly sensitive electrochemical detection of thrombin via the amplification of graphene

Herein, we successfully fabricated a highly sensitive label-free electrochemical aptasensor for thrombin based on the amplification of graphene (Gra). The excellent electrochemical probe of nickel hexacyanoferrate nanoparticles (NiHCFNPs) was introduced to form Nafion-Graphene-NiHCFNPs (Nf-Gra-NiHCFNPs) nanocomposites membrane on the gold electrode. The employment of graphene not only enhanced the surface area of the electrode with increased NiHCFNPs immobilization, but also improved the conductivity of the electrode, which further effectively improved the sensitivity of this proposed aptasensor. Subsequently, AuNPs layer was formed to immobilize the thrombin aptamer (TBA) and enhance the stability of the composite monolayer mentioned above. Then, thiol-modified TBA was assembled onto the AuNPs layer. Thereafter, hexanethiol (HT) was employed to block the possible remaining active sites. With the dual amplification of Gra and AuNPs, the resulting aptasensor exhibited good current response to target thrombin with a wide linear range extended from 1 pM to 80 nM (the detection limit was 0.3 pM). Additionally, the morphologies of bare Au substrate, nickel hexacyanoferrate nanoparticles (NiHCFNPs) and nanocomposites were successfully characterized by atomic force microscopy (AFM).

Label-free fluorescent detection of ions, proteins, and small molecules using structure-switching aptamers, SYBR Gold, and exonuclease I

We have demonstrated a label-free sensing strategy employing structure-switching aptamers (SSAs), SYBR Gold, and exonuclease I to detect a broad range of targets including inorganic ions, proteins, and small molecules. This nearly universal biosensor approach is based on the observation that SSAs at binding state with their targets, which fold into secondary structures such as quadruplex structure or Y shape structure, show more resistance to nuclease digestion than SSAs at unfolded states. The amount of aptamer left after nuclease reaction is proportional to the concentrations of the targets and in turn is proportional to the fluorescence intensities from SYBR Gold that can only stain nucleic acids but not their digestion products, nucleoside monophosphates (dNMPs). Fluorescent assays employing this mechanism for the detection of potassium ion (K(+)) are sensitive, selective, and convenient. Twenty μM K(+) is readily detected even at the presence of a 500-fold excess of Na(+). Likewise, we have generalized the approach to the specific and convenient detection of proteins (thrombin) and small molecules (cocaine). The assays were then validated by detecting K(+), cocaine, and thrombin in urine and serum or cutting and masking adulterants with good agreements with the true values. Compared to other reported approaches, most limited to G-quadruplex structures, the demonstrated method has less structure requirements of both the SSAs and their complexes with targets, therefore rending its wilder applications for various targets. The detection scheme could be easily modified and extended to detection platforms to further improve the detection sensitivity or for other applications as well as being useful in high-throughput and paralleled analysis of multiple targets.

Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection

We demonstrate highly sensitive and selective potassium ion detection against excess sodium ions in water, by modulating the interaction between the G-quadruplex-forming molecular beacon aptamer (MBA) and cationic conjugated polyelectrolyte (CPE). The K(+)-specific aptamer sequence in MBA is used as the molecular recognition element, and the high binding specificity of MBA for potassium ions offers selectivity against a range of metal ions. The hairpin-type MBA labeled with a fluorophore and quencher at both termini undergoes a conformational change (by complexation with CPEs) to either an open-chain form or a G-quadruplex in the absence or presence of K(+) ions. Conformational changes of MBA as well as fluorescence (of the fluorophore in MBA) quenching or amplification via fluorescence resonance energy transfer from CPEs provide clear signal turn-off and -on in the presence or absence of K(+). The detection limit of the K(+) assays is determined to be ~1.5 nM in the presence of 100 mM Na(+) ions, which is ~3 orders of magnitude lower than those reported previously. The successful detection of 5'-adenosine triphosphate (ATP) with the MBA containing an ATP-specific aptamer sequence is also demonstrated using the same sensor scheme. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.

Hierarchical dendritic gold microstructure-based aptasensor for ultrasensitive electrochemical detection of thrombin using functionalized mesoporous silica nanospheres as signal tags

A sensitive electrochemical approach for the detection of thrombin was designed by using densely packed hierarchical dendritic gold microstructures (HDGMs) with secondary and tertiary branches as matrices, and thionine-functionalized mesoporous silica nanospheres as signal tags. To prepare the signal tags, the positively charged thionine (as an indicator) was initially adsorbed onto the mesoporous silica nanoparticles (MSNs). Then [AuCl(4)](-) ions were in situ reduced on the thionine-modified MSNs by ascorbic acid to construct nanogold-decorated MSNs (GMSNs). The formed GMSNs were employed as label of the aminated aptamers. The assay was carried out in PBS, pH 7.4 with a sandwich-type assay mode by using the assembled thionine in the GMSNs as indicators. Compared with the pure silica nanoparticles, mesoporous silica could provide a larger surface for the immobilization of biomolecules and improve the sensitivity of the aptasensor. Under optimal conditions, the electrochemical aptasensors exhibited a wide linear range from 0.001 to 600 ng mL(-1) (i.e. 0.03 pM to 0.018 μM thrombin) with a low detection limit (LOD) of 0.5 pg mL(-1) (≈15 fM) thrombin at 3σ. No obvious non-specific adsorption was observed during a series of analyses to detect target analyte. The precision, selectivity and stability of the aptasensors were acceptable. Importantly, the methodology was evaluated with thrombin spiked samples in blank fetal calf serum, and the recoveries were 94.2-112%, indicating an exciting potential for thrombin detection.

Metal ion sensors based on DNAzymes and related DNA molecules

Metal ion sensors are an important yet challenging field in analytical chemistry. Despite much effort, only a limited number of metal ion sensors are available for practical use because sensor design is often a trial-and-error-dependent process. DNAzyme-based sensors, in contrast, can be developed through a systematic selection that is generalizable for a wide range of metal ions. Here, we summarize recent progress in the design of DNAzyme-based fluorescent, colorimetric, and electrochemical sensors for metal ions, such as Pb(2+), Cu(2+), Hg(2+), and UO(2)(2+). In addition, we also describe metal ion sensors based on related DNA molecules, including T-T or C-C mismatches and G-quadruplexes.