Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

Enhanced SELEX Platforms for Aptamer Selection with Improved Characteristics: A Review

This review delves into the advancements in molecular recognition through enhanced SELEX (Systematic Evolution of Ligands by Exponential Enrichment) platforms and post-aptamer modifications. Aptamers, with their superior specificity and affinity compared to antibodies, are central to this discussion. Despite the advantages of the SELEX process-encompassing stages like ssDNA library preparation, incubation, separation, and PCR amplification-it faces challenges, such as nuclease susceptibility. To address these issues and propel aptamer technology forward, we examine next-generation SELEX platforms, including microfluidic-based SELEX, capillary electrophoresis SELEX, cell-based aptamer selection, counter-SELEX, in vivo SELEX, and high-throughput sequencing SELEX, highlighting their respective merits and innovations. Furthermore, this article underscores the significance of post-aptamer modifications, particularly chemical strategies that enhance aptamer stability, reduce renal filtration, and expand their target range, thereby broadening their utility in diagnostics, therapeutics, and nanotechnology. By synthesizing these advanced SELEX platforms and modifications, this review illuminates the dynamic progress in aptamer research and outlines the ongoing efforts to surmount existing challenges and enhance their clinical applicability, charting a path for future breakthroughs in this evolving field.

Optimization of Surface-Enhanced Raman Spectroscopy Detection Conditions for Interaction between Gonyautoxin and Its Aptamer

This study aimed to optimize the detection conditions for surface-enhanced Raman spectroscopy (SERS) of single-stranded DNA (ssDNA) in four different buffers and explore the interaction between gonyautoxin (GTX1/4) and its aptamer, GO18. The influence of the silver colloid solution and MgSO₄ concentration (0.01 M) added under four different buffered conditions on DNA SERS detection was studied to determine the optimum detection conditions. We explored the interaction between GTX1/4 and GO18 under the same conditions as those in the systematic evolution of ligands by exponential enrichment technique, using Tris-HCl as the buffer. The characteristic peaks of GO18 and its G-quadruplex were detected in four different buffer solutions. The change in peak intensity at 1656 cm⁻¹ confirmed that the binding site between GTX1/4 and GO18 was in the G-quadruplex plane. The relative intensity of the peak at 1656 cm⁻¹ was selected for the GTX1/4–GO18 complex (I₁₆₅₆/I₁₀₉₉) to plot the ratio of GTX1/4 in the Tris-HCl buffer condition (including 30 μL of silver colloid solution and 2 μL of MgSO₄), and a linear relationship was obtained as follows: Y = 0.1867X + 1.2205 (R² = 0.9239). This study provides a basis for subsequent application of SERS in the detection of ssDNA, as well as the binding of small toxins and aptamers.

Aptamer-Modified Hydrogels

Hydrogels have attracted much attention especially due to their biocompatibility and their potential for stimulus responsiveness. By combining hydrogels with aptamers, biological recognition and responsiveness can be added to hydrogels, thereby opening path to advanced applications in biosensing and biomedicine. Within this chapter aptamers will be introduced and their contributions to biological responsiveness of hydrogels will be described. Especially the aptamer-based mechanisms that result in biological responsiveness will be explained and examples for the application of these mechanisms will be given ranging from rather simple sensing approaches to advanced materials for tissue engineering and drug delivery. Since aptamers are not only highly specific bioreceptors, but represent switchable structures that can be easily manipulated using well-known DNA techniques, the combination of aptamers and hydrogels facilitates the rational design of well-programmable and target-responsive smart hydrogels.

New electrochemical method for programmed death-ligand 1 detection based on a paper-based microfluidic aptasensor

As programmed death-ligand 1 (PD-L1) is considered a referenced therapeutic biomarker, a rapid and low-cost method to detect PD-L1 in body fluids is necessary. In this work, a paper-based microfluidic aptasensor for label-free electrochemical detection of PD-L1 in liquids was fabricated. The aptasensor integrates a reaction cell and a three-electrode system, and a differential pulse voltammetry electrochemical method was adopted. PD-L1 aptamer with a low equilibrium dissociation constant was used as a biorecognition molecule. To bind the aptamer and assist in the electrochemical measurement, nanocomposites were synthesized and used to modify the working electrode, which was composed of an amine-functionalized single-walled carbon nanotube, new methylene blue and gold nanoparticles. The basic performance of the aptasensor was tested in phosphate-buffered saline: the linear range was between 10 pg mL^-1 and 2.5 ng mL^-1, and the detection limit was 10 pg mL^-1 (signal/noise = 3). Moreover, the aptasensor was used for the detection of serum samples and compared with an enzyme linked immunosorbent assay (ELISA). The results showed that the aptasensor provides a new low-cost, portable and highly sensitive detection method for PD-L1, as an alternative to ELISA.

Analysis of the role played by ligand-induced folding of the cocaine-binding aptamer in the photochrome aptamer switch assay

The Photochrome Aptamer Switch Assay (PHASA) relies on ligand binding by an aptamer to alter the local environment of a stilbene compound covalently attached to the 5' end of the aptamer. We used the PHASA with both structure switching and non-structure switching versions of the cocaine-binding aptamer. We show that the largest change in fluorescence intensity and the lowest concentration limit of detection (C_Loo_D) is obtained using the structure-switching cocaine-binding aptamer. Fluorescence anisotropy measurements were used to quantify the affinity of the conjugated aptamer to cocaine. We also used thermal melt analysis and Nuclear Magnetic Resonance (NMR) spectroscopy to show that the addition of the stilbene to the aptamer increases the melt temperature of the cocaine-bound structure-switching aptamer by (6.4 ± 0.3) °C compared to the unconjugated aptamer while the free form of the structure-switching aptamer-stilbene conjugate remains unfolded.

A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition

As a ubiquitous second messenger, cyclic adenosine monophosphate (cAMP) mediates diverse biological processes such as cell growth, inflammation, and metabolism. The ability to probe these pathways would be significantly enhanced if we had a DNA-based sensor for cAMP. Herein, we describe a new, 31-base long single-stranded DNA aptamer for cAMP, denoted caDNApt-1, that was isolated by in vitro selection using systemic evolution of ligands after exponential enrichment (SELEX). caDNApt-1 has an approximately threefold higher affinity for cAMP than ATP, ADP, and AMP. Using non-denaturing gel electrophoresis and fluorescence spectroscopy, we characterized the structural changes caDNApt-1 undergoes upon binding to cAMP and revealed its potential as a cAMP sensor.

Recent trends in electrochemiluminescence aptasensors and their applications

Aptamers are single stranded DNA or RNA ligands which can be selected for different targets from proteins to small organic dyes. In the past few years great progress has been accomplished in the development of aptamer based bioanalytical assays with different detection techniques. Among them, electrochemiluminescence (ECL) aptasensors are very promising because they have the advantages of both electrochemical and chemiluminescence biosensors, such as high sensitivity, low background, cost effectiveness, and ease of control. In this review, we summarize the recent efforts to construct novel and improved ECL aptasensors and their application.

Immunochromatographic strip biosensor for the rapid detection of N-glycolylneuraminic acid based on aptamer-conjugated nanoparticle

N-glycolylneuraminic acid (Neu5Gc) is a type of sialic acid that is not typically produced in healthy humans but detective in some visceral cancer cells. As a new carcinoma biomarker, the level change in the serum and urine from the patient could potentially have the relation to the disease progression. So the measurement of the Neu5Gc will help to take a better response to therapeutic schedule for the sufferers. A sensitive and rapid aptamer-nanoparticle immunochromatographic strip for the visual detection of Neu5Gc was developed. The assay is based on the competitive reaction of binding the DNA aptamer targeting the candidate molecule selected by SELEX between Neu5Gc and complementary DNA. The sensing results indicated that the aptamer-based strip was sufficiently sensitive to detect Neu5Gc. The visual limit of detection (LOD) for semi-quantitative detection was 30 ng/mL under the optimal conditions and a quantitative detection limit of 5.38 ng/mL could be obtained using a scanning strip reader. The average recovery of the spiked cancer cell samples was 88.86%, with a coefficient of variation (CV) of 5.27%. The detection could be performed in less than 15 min using a simple procedure without any complicated equipment, demonstrating that this aptamer-nanoparticle biosensor strip has great potential for use to Neu5Gc-related cancer diagnosis.

Optimizing Stem Length To Improve Ligand Selectivity in a Structure-Switching Cocaine-Binding Aptamer

Understanding how aptamer structure and function are related is crucial in the design and development of aptamer-based biosensors. We have analyzed a series of cocaine-binding aptamers with different lengths of their stem 1 in order to understand the role that this stem plays in the ligand-induced structure-switching binding mechanism utilized in many of the sensor applications of this aptamer. In the cocaine-binding aptamer, the length of stem 1 controls whether the structure-switching binding mechanism for this aptamer occurs or not. We varied the length of stem 1 from being one to seven base pairs long and found that the structural transition from unfolded to folded in the unbound aptamer is when the aptamer elongates from 3 to 4 base pairs in stem 1. We then used this knowledge to achieve new binding selectivity of this aptamer for quinine over cocaine by using an aptamer with a stem 1 two base pairs long. This selectivity is achieved by means of the greater affinity quinine has for the aptamer compared with cocaine. Quinine provides enough free energy to both fold and bind the 2-base pair-long aptamer while cocaine does not. This tuning of binding selectivity of an aptamer by reducing its stability is likely a general mechanism that could be used to tune aptamer specificity for tighter binding ligands.

Development of a thermal-stable structure-switching cocaine-binding aptamer

We have developed a new cocaine-binding aptamer variant that has a significantly higher melt temperature when bound to a ligand than the currently used sequence. Retained in this new construct is the ligand-induced structure-switching binding mechanism that is important in biosensing applications of the cocaine-binding aptamer. Isothermal titration calorimetry methods show that the binding affinity of this new sequence is slightly tighter than the existing cocaine-binding aptamer. The improved thermal performance, a T_m increase of 4 °C for the cocaine-bound aptamer and 9 °C for the quinine-bound aptamer, was achieved by optimizing the DNA sequence in stem 2 of the aptamer to have the highest stability based on the nearest neighbor thermodynamic parameters and confirmed by UV and fluorescence spectroscopy. The sequences in stem 1 and stem 3 were unchanged in order to retain the structure switching and ligand binding functions. The more favorable thermal stability characteristics of the OR3 aptamer should make it a useful construct for sensing applications employing the cocaine-binding aptamer system.

The Optimization and Characterization of an RNA-Cleaving Fluorogenic DNAzyme Probe for MDA-MB-231 Cell Detection

Breast cancer is one of the most frequently diagnosed cancers in females worldwide and lacks specific biomarkers for early detection. In a previous study, we obtained a selective RNA-cleaving Fluorogenic DNAzyme (RFD) probe against MDA-MB-231 cells, typical breast cancer cells, through the systematic evolution of ligands by exponential process (SELEX). To improve the performance of this probe for actual application, we carried out a series of optimization experiments on the pH value of a reaction buffer, the type and concentration of cofactor ions, and sequence minimization. The length of the active domain of the probe reduced to 25 nt from 40 nt after optimization, which was synthesized more easily and economically. The detection limit of the optimized assay system was 2000 MDA-MB-231 cells in 30 min, which is more sensitive than the previous one (almost 5000 cells). The DNAzyme probe was also capable of distinguishing MDA-MB-231 cell specifically from 3 normal cells and 10 other tumor cells. This probe with high sensitivity, selectivity, and economic efficiency enhances the feasibility for further clinical application in breast cancer diagnosis. Herein, we developed an optimization system to produce a general strategy to establish an easy-to-use DNAzyme-based assay for other targets.

Sensitive fluorescence detection of ATP based on host-guest recognition between near-infrared β-Cyclodextrin-CuInS2 QDs and aptamer

We have developed a near-infrared (NIR) fluorescent aptamer-based sensor for sensitive detection of adenosine-5'-triphosphate (ATP) by using a ATP-binding aptamer and β-Cyclodextrin-CuInS₂ quantum dots (β-CD-CuInS₂ QDs). The fluorescence of β-CD-CuInS₂ QDs has a slight enhancement with the addition of ATP-binding aptamer due to the host-guest recognition between aptamer and β-CD. When ATP is added, it will bind to aptamer to form G-quadruplexes. Aptamer-ATP complexes can enter into the hydrophobic cavities of β-CD and result in great enhancement of the fluorescence intensity. Under the optimum conditions, the fluorescence intensity of β-CD-CuInS₂ QDs is proportional to the concentration of ATP, which shows a good linear response toward ATP concentration range of 6-1200μmolL^-1, the detection limit for ATP is 3μmolL^-1. The present assay shows a good selectivity for ATP over other biologically important proteins, and it is applied to the determination of ATP in human serum sample with satisfactory results.

Utilizing a Key Aptamer Structure-Switching Mechanism for the Ultrahigh Frequency Detection of Cocaine

Aptasensing of small molecules remains a challenge as detection often requires the use of labels or signal amplification methodologies, resulting in both difficult-to-prepare sensor platforms and multistep, complex assays. Furthermore, many aptasensors rely on the binding mechanism or structural changes associated with target capture by the aptameric probe, resulting in a detection scheme customized to each aptamer. It is in this context that we report herein a sensitive cocaine aptasensor that offers both real-time and label-free measurement capabilities. Detection relies on the electromagnetic piezoelectric acoustic sensor (EMPAS) platform. The sensing interface consists of a S-(11-trichlorosilyl-undecanyl)benzenethiosulfonate (BTS) adlayer-coated quartz disc onto which a structure-switching cocaine aptamer (MN6) is immobilized, completing the preparation of the MN6 cocaine aptasensor (M6CA). The EMPAS system has recently been employed as the foundation of a cocaine aptasensor based on a structurally rigid cocaine aptamer variant (MN4), an aptasensor referred to by analogy as M4CA. M6CA represents a significant increase in terms of analytical performance, compared to not only M4CA but also other cocaine aptamer-based sensors that do not rely on signal amplification, producing an apparent K(d) of 27 ± 6 μM and a 0.3 μM detection limit. Remarkably, the latter is in the range of that achieved by cocaine aptasensors relying on signal amplification. Furthermore, M6CA proved to be capable not only of regaining its cocaine-binding ability via simple buffer flow over the sensing interface (i.e., without the necessity to implement an additional regeneration step, such as in the case of M4CA), but also of detecting cocaine in a multicomponent matrix possessing potentially assay-interfering species. Finally, through observation of the distinct shape of its response profiles to cocaine injection, demonstration was made that the EMPAS system in practice offers the possibility to distinguish between the binding mechanisms of structure-switching (MN6) vs rigid (MN4) aptameric probes, an ability that could allow the EMPAS to provide a more universal aptasensing platform than what is ordinarily observed in the literature.

Ultra-high frequency piezoelectric aptasensor for the label-free detection of cocaine

This paper describes a label-free and real-time piezoelectric aptasensor for the detection of cocaine. The acoustic wave sensing platform is a quartz substrate functionalized with an adlayer of S-(11-trichlorosilyl-undecanyl)-benzenethiosulfonate (BTS) cross-linker onto which the anti-cocaine MN4 DNA aptamer is next immobilized. Preparation of the sensor surface was monitored using X-ray photoelectron spectroscopy (XPS), while the binding of cocaine to surface-attached MN4 was evaluated using the electromagnetic piezoelectric acoustic sensor (EMPAS). The MN4 aptamer, unlike other cocaine aptamer variants, has its secondary structure preformed in the unbound state with only tertiary structure changes occurring during target binding. It is postulated that the highly sensitive EMPAS detected the binding of cocaine through target mass loading coupled to aptamer tertiary structure folding. The sensor achieved an apparent Kd of 45 ± 12 µM, and a limit of detection of 0.9 µM. Repeated regenerability of the sensor platform was also demonstrated. This work constitutes the first application of EMPAS technology in the field of aptasensors. Furthermore, it is so far one of the very few examples of a bulk acoustic wave aptasensor that is able to directly detect the binding interaction between an aptamer and a small molecule in a facile one-step protocol without the use of a complex assay or signal amplification step.

Quinine binding by the cocaine-binding aptamer. Thermodynamic and hydrodynamic analysis of high-affinity binding of an off-target ligand

The cocaine-binding aptamer is unusual in that it tightly binds molecules other than the ligand it was selected for. Here, we study the interaction of the cocaine-binding aptamer with one of these off-target ligands, quinine. Isothermal titration calorimetry was used to quantify the quinine-binding affinity and thermodynamics of a set of sequence variants of the cocaine-binding aptamer. We find that the affinity of the cocaine-binding aptamer for quinine is 30-40 times stronger than it is for cocaine. Competitive-binding studies demonstrate that both quinine and cocaine bind at the same site on the aptamer. The ligand-induced structural-switching binding mechanism of an aptamer variant that contains three base pairs in stem 1 is retained with quinine as a ligand. The short stem 1 aptamer is unfolded or loosely folded in the free form and becomes folded when bound to quinine. This folding is confirmed by NMR spectroscopy and by the short stem 1 construct having a more negative change in heat capacity of quinine binding than is seen when stem 1 has six base pairs. Small-angle X-ray scattering (SAXS) studies of the free aptamer and both the quinine- and the cocaine-bound forms show that, for the long stem 1 aptamers, the three forms display similar hydrodynamic properties, and the ab initio shape reconstruction structures are very similar. For the short stem 1 aptamer there is a greater variation among the SAXS-derived ab initio shape reconstruction structures, consistent with the changes expected with its structural-switching binding mechanism.

Cocaine detection by structure-switch aptamer-based capillary zone electrophoresis

Aptamers, which are nucleic acid oligonucleotides that can bind targets with high affinity and specificity, have been widely applied as affinity probes in capillary electrophoresis (CE). Due to relative weak interaction between aptamers and small molecules, the application of aptamer-based CE is still limited in certain compounds. A new strategy that is based on the aptamer structure-switch concept was designed for small molecule detection by a novel CE method. A carboxyfluorescein (fluorescein amidite, FAM) label DNA aptamer was first incubated with partial complementary strand (CS), and then the free aptamer and the aptamer-CS duplex were well separated and determined by metal cation mediated CE/laser-induced fluorescence. When the target was introduced into the incubated sample, the hybridized form was destabilized, resulting in the changes of the fluorescence intensities of the free aptamer and the aptamer-CS duplex. The length of CS was investigated and 12 mer CS showed the best sensitivity for the detection of cocaine. The presented CE-LIF method, which combines the separation power of CE with the specificity of interactions occurring between target, aptamer, and CS, could be a universal detection strategy for other aptamer-specified small molecules.

Enzyme-linked small-molecule detection using split aptamer ligation

Here we report an aptamer-based analogue of the widely used sandwich enzyme-linked immunosorbent assay (ELISA). This assay utilizes the cocaine split aptamer, which is comprised of two DNA strands that only assemble in the presence of the target small molecule. One split aptamer fragment is immobilized on a microplate, then a test sample is added containing the second split aptamer fragment. If cocaine is present in the test sample, it directs assembly of the split aptamer and promotes a chemical ligation between azide and cyclooctyne functional groups appended to the termini of the split aptamer fragments. Ligation results in covalent attachment of biotin to the microplate and provides a colorimetric output upon conjugation to streptavidin-horseradish peroxidase. Using this assay, we demonstrate detection of cocaine at concentrations of 100 nM-100 μM in buffer and 1-100 μM human blood serum. The detection limit of 1 μM in serum represents an improvement of two orders of magnitude over previously reported split aptamer-based sensors and highlights the utility of covalently trapping split aptamer assembly events.

Aptamer sensor for cocaine using minor groove binder based energy transfer

We report on an optical aptamer sensor for cocaine detection. The cocaine sensitive fluorescein isothiocyanate (FITC)-labeled aptamer underwent a conformational change from a partial single-stranded DNA with a short hairpin to a double-stranded T-junction in the presence of the target. The DNA minor groove binder Hoechst 33342 selectively bound to the double-stranded T-junction, bringing the dye within the Förster radius of FITC, and therefore initiating minor groove binder based energy transfer (MBET), and reporting on the presence of cocaine. The sensor showed a detection limit of 0.2 μM. The sensor was also implemented on a carboxy-functionalized polydimethylsiloxane (PDMS) surface by covalently immobilizing DNA aptamers. The ability of surface-bound cocaine detection is crucial for the development of microfluidic sensors.

Engineering a structure switching mechanism into a steroid-binding aptamer and hydrodynamic analysis of the ligand binding mechanism

The steroid binding mechanism of a DNA aptamer was studied using isothermal titration calorimetry (ITC), NMR spectroscopy, quasi-elastic light scattering (QELS), and small-angle X-ray spectroscopy (SAXS). Binding affinity determination of a series of steroid-binding aptamers derived from a parent cocaine-binding aptamer demonstrates that substituting a GA base pair with a GC base pair governs the switch in binding specificity from cocaine to the steroid deoxycholic acid (DCA). Binding of DCA to all aptamers is an enthalpically driven process with an unfavorable binding entropy. We engineered into the steroid-binding aptamer a ligand-induced folding mechanism by shortening the terminal stem by two base pairs. NMR methods were used to demonstrate that there is a transition from a state where base pairs are formed in one stem of the free aptamer, to where three stems are formed in the DCA-bound aptamer. The ability to generate a ligand-induced folding mechanism into a DNA aptamer architecture based on the three-way junction of the cocaine-binding aptamer opens the door to obtaining a series of aptamers all with ligand-induced folding mechanisms but triggered by different ligands. Hydrodynamic data from diffusion NMR spectroscopy, QELS, and SAXS show that for the aptamer with the full-length terminal stem there is a small amount of structure compaction with DCA binding. For ligand binding by the short terminal stem aptamer, we propose a binding mechanism where secondary structure forms upon DCA binding starting from a free structure where the aptamer exists in a compact form.

Electrogenerated chemiluminescence detection of mercury(II) ions based on DNA probe labeled with ruthenium complex

A novel mercury(II) ion (Hg(2+)) biosensor with electrogenerated chemiluminescence (ECL) detection using tris(2,2'-bipyridyl) ruthenium derivatives (ruthenium complex) as labeling was developed in the prescent work. One thymine (T)-rich single-strand DNA (ssDNA) labeled with a ruthenium complex was taken as an ECL probe. When the other T-rich capture ssDNA was self-assembled onto the surface of a gold electrode with a thiol group, and then hybridized with the ECL probe to form double-strand DNA (dsDNA) structures in the presence of Hg(2+), a strong ECL response was electrochemically generated. The ECL intensity was linearly related to the concentration of Hg(2+) in the range from 1.0 × 10(-6) to 1 × 10(-9) M with a detection limit of 3.0 × 10(-10) M. The relative standard deviation was 4.1% at 1.0 × 10(-7) M Hg(2+) (n = 5). This work demonstrates that the combination of the strongly binding T-rich DNA to Hg(2+) with the highly sensitive ECL technique to design an ECL Hg(2+) biosensor is a great promising approach for the determination of metal ions.

Small-molecule-dependent split aptamer ligation

Here we describe the first use of small-molecule binding to direct a chemical reaction between two nucleic acid strands. The reported reaction is a ligation between two fragments of a DNA split aptamer using strain-promoted azide-alkyne cycloaddition. Utilizing the split aptamer for cocaine, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of cocaine concentrations and is compatible with complex biological fluids such as human blood serum. Moreover, studies of split aptamer ligation at varying salt concentrations and using structurally similar analogues of cocaine have revealed new insight into the assembly and small-molecule binding properties of the cocaine split aptamer. The ability to translate the presence of a small-molecule target into the output of DNA ligation is anticipated to enable the development of new, broadly applicable small-molecule detection assays.

ssDNA aptamer-based column for simultaneous removal of nanogram per liter level of illicit and analgesic pharmaceuticals in drinking water

Aptamers are a new class of single-stranded DNA/RNA molecules selected from synthetic nucleic acid libraries for molecular recognition. Our group reports a novel aptamer column for the removal of trace (ng/L) pharmaceuticals in drinking water. In this study, cocaine and diclofenac were chosen as model molecules to test the aptamer column which presented high removal capacity, selectivity, and stability. The removal of pharmaceuticals was as high as 88-95%. The data of adsorption were fitted with Langmuir isotherm and a pseudo-second-order kinetic model. A thermodynamic experiment proved the adsorption processes were exothermic in spontaneity. The kinetics of aptamer was composed of three steps: activation, binding, and hybridization. The first step was the rate-controlling step. The adsorption system was divided into three parts: kinetic, mixed, and thermodynamic zones from 0% to 100% binding fraction of aptamer. Furthermore, the aptamer column was reusable and achieved strong removal efficiency from 4 to 30 °C at normal cation ion concentration (5-100 mg/L) for multipollutants without cross effects and secondary pollution. This work indicates that aptamer, as a new sorbent, can be used in the removal of persistent organic pollutants, biological toxins, and pathogenic bacteria from surface, drinking, and ground water.

Novel extraction supports based on immobilised aptamers: evaluation for the selective extraction of cocaine

A new kind of selective sorbent based on the use of aptamers and dedicated to the selective solid phase extraction was developed. Cocaine aptamer was chosen as model aptamer to demonstrate the feasibility of this material and to provide a complete evaluation of the synthesized sorbent. The effect of different parameters such as the nature of the immobilisation support (silica, agarose), the type of immobilisation (covalent or non-covalent) and the length of the spacer arm (C(6) or C(12)) were studied. Therefore, various oligosorbents based on different immobilisation strategies were synthesized and characterised by estimating the extraction recovery and the capacity of cocaine and the binding efficiency of aptamers. Control supports without immobilised aptamers were simultaneously studied in parallel to assess the selectivity brought by the oligosorbents. The oligosorbent based on CNBr-activated sepharose showed the best performances with an extraction recovery for cocaine of 90% while 6% was obtained on the control sorbent. The high selectivity brought by the oligosorbent was then illustrated by applying the oligoextraction followed by LC/MS analysis to a post-mortem blood (cocaine overdose). Results were compared to those resulting from a conventional protein precipitation procedure. The presence of co-extracted interfering compounds was strongly reduced with the treatment by oligoextraction. A limit of quantification of 0.5 ng/mL was obtained that is largely lower than the concentration found after a single intake of cocaine.

Electrochemiluminescence in bioanalysis

The discovery of electrochemiluminescence (ECL) and its development as a means of detection is truly a success story. Although studies describing ECL were published in the early 1960s, most studies using ECL as a means of detection were not widely published until the mid 1990s. Incorporating ECL into assays provides increased sensitivity, several logs of dynamic range and the ability to electronically control the reaction. These characteristics provide advantages over assays that rely on radioisotopic labels, fluorescence and enzymatic activity. There have been many areas of science that have benefited from the use of ECL, including environmental microbiology, virology, neurobiology, molecular biology and immunology. ECL has improved the understanding and treatment of infectious diseases, cancer, neurodegenerative diseases and even sleep apnea disorders. Drug development has also benefited from ECL via improved assessment of pharmacodynamics, pharmacokinetics and determining immune responses against protein-based therapeutics. This review provides an overview of ECL chemistry and principles with a more detailed emphasis on the applications of ECL-based assays in different areas of science and medicine. The primary purpose of this review is to provide an in-depth discussion of the impact that ECL-based analysis has had on microbiology, immunology, virology, neurodegenerative diseases, molecular biology and drug development. Examples of ECL-based bioanalysis in each of these fields are discussed in conjunction with an overview of ECL principles and instrumentation.

Parallel G-quadruplex-specific fluorescent probe for monitoring DNA structural changes and label-free detection of potassium ion

Here we demonstrate an anionic porphyrin, protoporphyrin IX (PPIX), as a parallel G-quadruplex-specific fluorescent probe for monitoring DNA structural changes and utilize it to develop a DNA-based K(+) sensor. The interactions of PPIX with different DNA structures in K(+) or Na(+) solution are investigated by using circular dichroism, fluorescence, and UV-vis spectroscopy. The observations reveal that PPIX has an ∼100-fold selectivity for parallel G-quadruplexes against duplexes and antiparallel G-quadruplexes. Meanwhile, the fluorescence intensity of PPIX increases by over 10-fold upon binding to parallel G-quadruplexes. On the basis of the selectivity and fluorescence property of PPIX, we introduce a facile, label-free approach to monitoring DNA structural changes via fluorescence signal readout that is tuned by PPIX binding and release. To illustrate it, we utilize PPIX and a G-rich DNA PS2.M to construct a fluorescent K(+) sensor based on an antiparallel-to-parallel conformation transition of the G-quadruplex. PS2.M adopts an antiparallel quadruplex structure in Na(+) solution, whereas it gradually converts into a parallel G-quadruplex upon addition of increasing K(+). This conformational change is indicated by a sharp increase in the fluorescence intensity of PPIX, owing to the good ability of PPIX to discriminate parallel G-quadruplexes from antiparallel ones. Even in the presence of 100 mM Na(+), such a "turn-on" fluorescent sensor can respond to low concentrations of K(+), with a limit of detection (0.5 mM) for K(+) analysis. In addition, this sensor exhibits a high selectivity for K(+) over other common metal ions, which ensures its practical applications to real samples. These results reveal that PPIX is promising for use as a specific DNA structural probe in sensing applications.

Chemiluminescence and electrochemiluminescence detection of controlled drugs

We review the determination of various controlled drugs (opioids, tranquilizers, stimulants, and hallucinogens) using flow-analysis methodologies (flow injection analysis, high performance liquid chromatography, capillary electrophoresis, and microfluidic devices) with chemiluminescence and electrochemiluminescence reagents such as luminol, diaryloxalates, tris(2,2'-bipyridine)ruthenium(II), permanganate, manganese(IV), and sulfite, for industrial, clinical, pharmaceutical, and forensic science applications.

Defining a stem length-dependent binding mechanism for the cocaine-binding aptamer. A combined NMR and calorimetry study

We have used a combined approach of NMR spectroscopy and isothermal titration calorimetry (ITC) to determine the ligand-binding mechanism employed by a cocaine-binding aptamer. We found that the length of the stem containing the 3' and 5' termini determines the nature of the binding mechanism. When this stem is six base pairs long, the secondary structure of the aptamer is fully folded in the free form and only putative tertiary interactions form with ligand binding. If this stem is shortened by three base pairs, the free form of the aptamer contains little secondary structure, and ligand binding triggers secondary structure formation and folding. This binding mechanism is supported by both NMR spectral changes and the ITC measured heat capacity of binding (ΔC(p)°). For the aptamer with the long stem the ΔC(p)° value is -557 ± 29 cal mol(-1) K(-1) and for the aptamer with the short stem the ΔC(p)° value is -922 ± 51 cal mol(-1) K(-1). Chemical shift perturbation data and the observation of intermolecular NOEs indicate that the three-way junction is the site of ligand binding.

Determination of cocaine in human plasma by selective solid-phase extraction using an aptamer-based sorbent

A complete characterization is presented of a highly selective solid-phase extraction (SPE) sorbent which exploits the properties of aptamers. An oligosorbent based on aptamers immobilized on a solid support was synthesized and tested for the selective extraction of cocaine from human plasma. Anticocaine aptamers were immobilized to CNBr-activated Sepharose, and an extraction procedure was developed in pure media. Specific retention of cocaine on the oligosorbent was demonstrated, and the capacity of the support was determined. This oligosorbent was then applied to the selective extraction of cocaine from plasma at a concentration of 0.4 mg L(-1), i.e., corresponding to the plasma concentration reached after an intake of a single dose of cocaine. Extraction recovery close to 90% was obtained. Moreover, interfering compounds that perturbed cocaine quantification when using a standard SPE sorbent were not retained on the oligosorbent, thus allowing fast and reliable analyses of plasma samples with an estimated limit of detection of 0.1 microg mL(-1).

Aptamer conjugated Mo(6)S(9-x)I(x) nanowires for direct and highly sensitive electrochemical sensing of thrombin

We demonstrate the use of a novel electrochemical sensing platform based on aptamer conjugated Mo(6)S(9-x)I(x) nanowires (MoSI NWs) for the highly sensitive detection of the blood clotting enzyme thrombin. MoSI NWs nanowires were self-assembled on a gold electrode to which thrombin binding aptamers were covalently attached. The modification and immobilization steps of the electrodes were characterised by cyclic voltammetry along with high-resolution transmission electron microscopy and X-ray photoelectron spectroscopy. The platform is based on the creation of a self-assembled MoSI MW layer via the sulfur-gold affinity followed by the creation of MoSI-thiolated aptamer conjugates via the sulfur-sulfur affinity. Using this system, sensitive quantitative detection of thrombin is realized by monitoring differences of differential pulse voltammetric responses of electrostatically trapped [Ru(NH(3))(6)](3+) cations to the aptamer before and after thrombin binding. The sensitivity limit for the detection of thrombin is 10 pM. This value is 10-fold better than all currently reported one step label free electrochemical strategies. Given the direct label free nature of the approach and the simplicity of the electronic detection, the aptamer conjugated MoSI NWs biosensor appears well suited for implementation in portable point of care microdevices directed at the rapid and sensitive detection of proteins and pathogens.

Aptamer-modified micellar electrokinetic chromatography for the enantioseparation of nucleotides

In this paper, a new aptamer-based capillary electrophoresis (CE) method, which was able to separate the enantiomers of an anionic target (adenosine monophosphate, AMP) displaying the same electrophoretic mobility as that of the oligonucleotidic chiral selector, is reported. The design of the aptamer-modified micellar electrokinetic chromatography (MEKC) mode consisted of nonionic micelles which acted as a pseudostationary phase and a hydrophobic cholesteryl group-tagged aptamer (Chol-Apt) which partitioned into the uncharged micellar phase. Under partial-filling format and suppressed electroosmotic flow conditions, the strong mobility alteration of Chol-Apt permitted AMP enantiomers to pass through the micelle-anchored aptamer zone and promoted the target enantioseparation. The influence of several electrophoretic parameters (such as concentration and nature of the nonionic surfactant, preincubation of the Chol-Apt and surfactant, capillary temperature, and applied voltage) on the AMP enantiomer migration was investigated in order to define the utilization conditions of the aptamer-modified MEKC mode. The chiral resolution, in a single run, of three adenine nucleotides, i.e., AMP, ADP (adenosine diphosphate), and ATP (adenosine triphosphate), was further accomplished using such methodology. This approach demonstrates the possibility to extend the CE applicability of aptamer chiral selectors to potentially any target, without restriction on its charge-to-mass ratio.

Label-free aptamer-based colorimetric detection of mercury ions in aqueous media using unmodified gold nanoparticles as colorimetric probe

We report a simple and sensitive aptamer-based colorimetric detection of mercury ions (Hg(2+)) using unmodified gold nanoparticles as colorimetric probe. It is based on the fact that bare gold nanoparticles interact differently with short single-strand DNA and double-stranded DNA. The anti-Hg(2+) aptamer is rich in thymine (T) and readily forms T-Hg(2+)-T configuration in the presence of Hg(2+). By measuring color change or adsorption ratio, the bare gold nanoparticles can effectively differentiate the Hg(2+)-induced conformational change of the aptamer in the presence of a given salt with high concentration. The assay shows a linear response toward Hg(2+) concentration through a five-decade range of 1 x 10(-4) mol L(-1) to 1 x 10(-9) mol L(-1). Even with the naked eye, we could identify micromolar Hg(2+) concentrations within minutes. By using the spectrometric method, the detection limit was improved to the nanomolar range (0.6 nM). The assay shows excellent selectivity for Hg(2+) over other metal cations including K(+), Ba(2+), Ni(2+), Pb(2+), Cu(2+), Cd(2+), Mg(2+), Ca(2+), Zn(2+), Al(3+), and Fe(3+). The major advantages of this Hg(2+) assay are its water-solubility, simplicity, low cost, visual colorimetry, and high sensitivity. This method provides a potentially useful tool for the Hg(2+) detection.

Competitive affinity capillary electrophoresis assay based on a "hybrid" pre-incubation/on-capillary mixing format using an enantioselective aptamer as affinity ligand

In this paper, we describe an aptamer-based competitive affinity CE (ACE) assay involving (i) the pre-incubation of the target (D-arginine) and the specific ligand (anti-D-arginine-L-RNA aptamer) before (ii) the competition with the labeled target (dansylated D-arginine) through an on-capillary mixing strategy. The effects of some critical operating parameters such as the applied voltage and the sample-aptamer mixture plug length on the assay sensitivity were investigated. The ACE assay appeared particularly dependent on the plug length of the pre-incubated sample-aptamer solution. It was shown that this "hybrid" strategy significantly improved the assay sensitivity relative to that obtained with a "full" on-capillary mixing approach.

Multifunctional label-free electrochemical biosensor based on an integrated aptamer

Aptamers, which are in vitro selected functional oligonucleotides, have been employed to design novel biosensors (i.e., aptasensors) due to their inherent selectivity, affinity, and their multifarious advantages over traditional recognition elements. In this work, we reported a multifunctional reusable label-free electrochemical biosensor based on an integrated aptamer for parallel detection of adenosine triphosphate (ATP) and alpha-thrombin, by using electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). A Au electrode as the sensing surface was modified with a part DNA duplex which contained a 5'-thiolated partly complementary strand (PCS) and a mixed aptamer (MBA). The unimolecular MBA contained small-molecule ATP binding aptamer (ABA) and also protein alpha-thrombin binding aptamer (TBA). Thus, the aptasensor could be used for detection of ATP and alpha-thrombin both. The detection limit of ATP was 1 x 10(-8) M, and its detection range could extend up to 10(-4) M, whereas the detection limit of alpha-thrombin was 1 x 10(-11) M, and its detection range was from 1 x 10(-11) to 1 x 10(-7) M. Meanwhile, after detecting alpha-thrombin, the sensing interface could be used for ATP recognition as well. The aptasensor regeneration could be realized by rehybridizing of the MBA strand with the partly complementary strand immobilized on the Au surface after ATP detection or by treating with a large amount of ATP and then rehybridizing the MBA strand with the partly complementary strand immobilized on the Au surface after alpha-thrombin detection. The aptasensor fabricated exhibited several advantages such as label-free detection, high sensitivity, regeneration, and multifunctional recognition. It also showed the detectability in biological fluid. Therein it held promising potential for integration of the sensing ability such as the simultaneous detection for multianalysis in the future.

Amplified electrochemical aptasensor taking AuNPs based sandwich sensing platform as a model

Here, we report a sensitive amplified electrochemical impedimetric aptasensor for thrombin, a kind of serine protease that plays important role in thrombosis and haemostasis. For improving detection sensitivity, a sandwich sensing platform is fabricated, in which the thiolated aptamers are firstly immobilized on a gold substrate to capture the thrombin molecules, and then the aptamer functionalized Au nanoparticles (AuNPs) are used to amplify the impedimetric signals. Such designed aptamer/thrombin/AuNPs sensing system could not only improve the detection sensitivity compared to the reported impedimetric aptasensors but also provide a promising signal amplified model for aptamer-based protein detection. In this paper, we realize a sensitive detection limit of 0.02 nM, with a linear range of 0.05-18 nM. Meanwhile, the effect of 6-mercaptohexanol (MCH) and 2-mercaptoethanol (MCE) on the modification of the electrode is investigated.

Reusable, label-free electrochemical aptasensor for sensitive detection of small molecules

We report a sensitive electrochemical aptasensor for adenosine based on electrochemical impedance spectroscopy measurement, which gives not only a label-free but also a reusable platform to make the detection of small molecules simple and convenient.