A DNA aptamer as a new target-specific chiral selector for HPLC

Optimisation of denaturing ion pair reversed phase HPLC for the purification of ssDNA in SELEX

Aptamers have shown great promise as oligonucleotide-based affinity ligands for various medicinal and industrial applications. A critical step in the production of DNA aptamers via selective enhancement of ligands by exponential enrichment (SELEX) is the generation of ssDNA from dsDNA. There are a number of caveats associated with current methods for ssDNA generation, which can lower success rates of SELEX experiments. They often result in low yields thereby decreasing diversity or fail to eliminate parasitic PCR by-products leading to accumulation of by-products from round to round. Both contribute to the failure of SELEX protocols and therefore potentially limit the impact of aptamers compared to their peptide-based antibody counterparts. We have developed a novel method using ion pair reversed phase HPLC (IP RP HPLC) employed under denaturing conditions for the ssDNA re-generation stage of SELEX following PCR. We have utilised a range of 5' chemical modifications on PCR primers to amplify PCR fragments prior to separation and purification of the DNA strands using denaturing IP RP HPLC. We have optimised mobile phases to enable complete denaturation of the dsDNA at moderate temperatures that circumvents the requirement of high temperatures and results in separation of the ssDNA based on differences in their hydrophobicity. Validation of the ssDNA isolation and purity assessment was performed by interfacing the IP RP HPLC with mass spectrometry and fluorescence-based detection. The results show that using a 5' Texas Red modification on the reverse primer in the PCR stage enabled purification of the ssDNA from its complimentary strand via IP RP HPLC under denaturing conditions. Additionally, we have confirmed the purity of the ssDNA generated as well as the complete denaturation of the PCR product via the use of mass-spectrometry and fluorescence analysis therefore proving the selective elimination of PCR by-products and the unwanted complementary strand. Following lyophilisation, ssDNA yields of up to 80% were obtained. In comparison the streptavidin biotin affinity chromatography also generates pure ssDNA with a yield of 55%. The application of this method to rapidly generate and purify ssDNA of the correct size, offers the opportunity to improve the development of new aptamers via SELEX.

Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin

The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.

Potential Universal Engineering Component: Tetracycline Response Nanoswitch Based on Triple Helix-Graphene Oxide

The overuse of antibiotics can lead to the emergence of drug resistance, preventing many common diseases from being effectively treated. Therefore, based on the special composite platform of P1/graphene oxide (GO) and DNA triple helix, a programmable DNA nanoswitch for the quantitative detection of tetracycline (TC) was designed. The introduction of GO as a quenching agent can effectively reduce the background fluorescence; stabilizing the trigger strand with a triplex structure minimizes errors. It is worth mentioning that the designed model has been verified and analyzed by both computer simulation and biological experiments. NUPACK predicts the combined mode and yield of each strand, while visual DSD flexibly predicts the changes in components over time during the reaction. The feasibility analysis preliminarily confirmed the realizability of the designed model, and the optimal reaction conditions were obtained through optimization, which laid the foundation for the subsequent quantitative detection of TC, while the selective experiments in different systems fully demonstrated that the model had excellent specificity.

A perspective on oligonucleotide therapy: Approaches to patient customization

It is estimated that the human genome encodes 15% of proteins that are considered to be disease-modifying. Only 2% of these proteins possess a druggable site that the approved clinical candidates target. Due to this disparity, there is an immense need to develop therapeutics that may better mitigate the disease or disorders aroused by non-druggable and druggable proteins or enzymes. The recent surge in approved oligonucleotide therapeutics (OT) indicates the imminent potential of these therapies. Oligonucleotide-based therapeutics are of intermediate size with much-improved selectivity towards the target and fewer off-target effects than small molecules. The OTs include Antisense RNAs, MicroRNA (MIR), small interfering RNA (siRNA), and aptamers, which are currently being explored for their use in neurodegenerative disorders, cancer, and even orphan diseases. The present review is a congregated effort to present the past and present of OTs and the current efforts to make OTs for plausible future therapeutics. The review provides updated literature on the challenges and bottlenecks of OT and recent advancements in OT drug delivery. Further, this review deliberates on a newly emerging approach to personalized treatment for patients with rare and fatal diseases with OT.

Aptasensors versus immunosensors-Which will prevail?

Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.

Aptamer-Modified Cu2+-Functionalized C-Dots: Versatile Means to Improve Nanozyme Activities-"Aptananozymes"

The covalent linkage of aptamer binding sites to nanoparticle nanozymes is introduced as a versatile method to improve the catalytic activity of nanozymes by concentrating the reaction substrates at the catalytic nanozyme core, thereby emulating the binding and catalytic active-site functions of native enzymes. The concept is exemplified with the synthesis of Cu²⁺ ion-functionalized carbon dots (C-dots), modified with the dopamine binding aptamer (DBA) or the tyrosinamide binding aptamer (TBA), for the catalyzed oxidation of dopamine to aminochrome by H₂O₂ or the oxygenation of l-tyrosinamide to the catechol product, which is subsequently oxidized to amidodopachrome, in the presence of H₂O₂/ascorbate mixture. Sets of structurally functionalized DBA-modified Cu²⁺ ion-functionalized C-dots or sets of structurally functionalized TBA-modified Cu²⁺ ion-functionalized C-dots are introduced as nanozymes of superior catalytic activities (aptananozymes) toward the oxidation of dopamine or the oxygenation of l-tyrosinamide, respectively. The aptananozymes reveal enhanced catalytic activities as compared to the separated catalyst and respective aptamer constituents. The catalytic functions of the aptananozymes are controlled by the structure of the aptamer units linked to the Cu²⁺ ion-functionalized C-dots. In addition, the aptananozyme shows chiroselective catalytic functions demonstrated by the chiroselective-catalyzed oxidation of l/d-DOPA to l/d-dopachrome. Binding studies of the substrates to the different aptananozymes and mechanistic studies associated with the catalytic transformations are discussed.

Capillary electrophoresis-based methodology for screening of oligonucleotide aptamers

As a new molecular recognition element, oligonucleotide aptamer not only has higher affinity and specificity to target molecules, but also has the advantages of wide recognition range, in vitro synthesis and chemical stability compared with conventional antibodies. Since a kind of screening method termed systematic evolution of ligands by exponential enrichment (SELEX) was reported, scientists have extensively researched the methodology of how to highly and efficiently screen out aptamers from a library consisting of a large number of random oligonucleotides. Certainly capillary electrophoresis-based screening methodologies, including nonequilibrium capillary electrophoresis of equilibrium mixtures, equilibrium capillary electrophoresis of equilibrium mixtures, non-SELEX, ideal-filter capillary electrophoresis, capillary transient isotachophoresis, etc., are revolutionary. Compared with conventional SELEX, these capillary electrophoresis-based methodologies show incomparable advantages such as the single-round screening of aptamers and increased successful screening rate. Methodology studies on the screening process of aptamers are comprehensively reviewed.

Aptamer-Based Affinity Chromatography for Protein Extraction and Purification

Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.

Highly sensitive host-guest mode homogenous electrochemical thrombin signal amplification aptasensor based on tetraferrocene label

The development of sensitive and convenient detection methods to monitor thrombin without the use of enzymes or complex nanomaterials is highly desirable for the diagnosis of cardiovascular diseases. In this article, tetraferrocene was first synthesized and then a sensitive and homogeneous electrochemical aptasensor was developed for thrombin detection based on host-guest recognition between tetraferrocene and β-cyclodextrin (β-CD). In the absence of thrombin, the double stem-loop of thrombin aptamer (TBA) prevented tetraferrocenes labeled at both ends from entering the cavity of β-CD deposited on gold electrode surface. After binding with thrombin, the stem-loop structure of TBA opened and transformed into special G-quarter structure, forcing tetraferrocene into the cavity of β-CD. As a result, thrombin allowed eight ferrocene molecules to reach the gold electrode surface, greatly amplifying the response signal. The obtained aptasensors showed dynamic detection range from 4 pM to 12.5 nM with detection limit around 1.2 pM. Overall, the results indicate that the proposed aptasensors are promising for future rapid clinical detection of thrombin and development of signal amplification strategies for detection of various proteins.

An Enzyme- and Label-Free Fluorescence Aptasensor for Detection of Thrombin Based on Graphene Oxide and G-Quadruplex

An enzyme- and label-free aptamer-based assay is described for the determination of thrombin. A DNA strand (S) consisting of two parts was designed, where the first (Sa) is the thrombin-binding aptamer and the second (Se) is a G-quadruplex. In the absence of thrombin, Sa is readily adsorbed by graphene oxide (GO), which has a preference for ss-DNA rather than for ds-DNA. Upon the addition of the N-methyl-mesoporphyrin IX (NMM), its fluorescence (with excitation/emission at 399/610 nm) is quenched by GO. In contrast, in the presence of thrombin, the aptamer will bind thrombin, and thus, be separated from GO. As a result, fluorescence will be enhanced. The increase is linear in the 0.37 µM to 50 µM thrombin concentration range, and the detection limit is 0.37 nM. The method is highly selective over other proteins, cost-effective, and simple. In our perception, it represents a universal detection scheme that may be applied to other targets according to the proper choice of the aptamer sequence and formation of a suitable aptamer-target pair.

Ideal-Filter Capillary Electrophoresis (IFCE) Facilitates the One-Step Selection of Aptamers

Selection of aptamers from oligonucleotide libraries currently requires multiple rounds of alternating steps of partitioning of binders from nonbinders and enzymatic amplification of all collected oligonucleotides. Herein, we report a highly practical solution for reliable one-step selection of aptamers. We introduce partitioning by ideal-filter capillary electrophoresis (IFCE) in which binders and nonbinders move in the opposite directions. The efficiency of IFCE-based partitioning reaches 10⁹ , which is ten million times higher than that of typical solid-phase partitioning methods. One step of IFCE-based partitioning is sufficient for the selection of a high-affinity aptamer pool for a protein target. Partitioning by IFCE promises to become an indispensable tool for fast and robust selection of binders from different types of oligonucleotide libraries.

The development of biphasic chiral recognition in chiral separation

In chiral separation, enantioseparation factor is an important parameter which influences the resolution of enantiomers. In this current overview, a biphasic chiral recognition method is introduced to the readers. This method can significantly improve the enantioseparation factor in two-phase solvent through adding lipophilic and hydrophilic chiral selectors which have opposite chiral recognition ability to organic and aqueous phases, respectively. This overview presents the development and applications of biphasic chiral recognition in liquid-liquid extraction and counter current chromatography. It mainly focuses on the topics of mechanism, advantages and limitations, applications, and key factors of biphasic chiral recognition. In addition, the future outlook on development of biphasic chiral recognition also has been discussed in this overview.

High performance affinity chromatography and related separation methods for the analysis of biological and pharmaceutical agents

The last few decades have witnessed the development of many high-performance separation methods that use biologically related binding agents. The combination of HPLC with these binding agents results in a technique known as high performance affinity chromatography (HPAC). This review will discuss the general principles of HPAC and related techniques, with an emphasis on their use for the analysis of biological compounds and pharmaceutical agents. Various types of binding agents for these methods will be considered, including antibodies, immunoglobulin-binding proteins, aptamers, enzymes, lectins, transport proteins, lipids, and carbohydrates. Formats that will be discussed for these methods range from the direct detection of an analyte to indirect detection based on chromatographic immunoassays, as well as schemes based on analyte extraction or depletion, post-column detection, and multi-column systems. The use of biological agents in HPLC for chiral separations will also be considered, along with the use of HPAC as a tool to screen or study biological interactions. Various examples will be presented to illustrate these approaches and their applications in fields such as biochemistry, clinical chemistry, and pharmaceutical research.

Mirror-image aptamer kissing complex for arginine-vasopressin sensing

The recently reported aptamer kissing complex (AKC) strategy has allowed for the development of a new kind of sandwich-like sensing tools. Currently AKC assays have been only applied to low molecular weight molecules and their functionality in complex matrices remains challenging. The objective of the present study broken down into two sub-aims; exploring the propensity to broaden the scope of detectable analytes and designing a more robust system for potential applications to realistic samples. An all L-configuration aptaswitch module derived from a hairpin spiegelmer specific to a larger target, i.e. the arginine-vasopressin (AVP) hormone, was elaborated. The target-induced AKC formation in presence of a specific mirror-image RNA hairpin (L-aptakiss) probe were analyzed by using fluorescence anisotropy. The mirror-image kissing complex was successfully formed when the L-AVP target bound to the engineered L-aptaswitch element. It was also established that the use of methanol as cosolvent significantly improved the assay sensitivity through the stabilization of the ternary complex. Finally, the capability of the mirror-image method to operate in 10-fold diluted, untreated human serum was illustrated. The current work revealed that the AKC concept can be expanded to a wider range of targets and converted to a L-configuration sensing platform especially suitable for bioanalysis purposes.

Aptamer affinity ligands in protein chromatography

The present review deals with the place of single chain oligonucleotide ligands (aptamers) in affinity chromatography applied to proteins. Aptamers are not the only affinity ligands available but they represent an emerging and highly promising route that advantageously competes with antibodies in immunopurification processes. A historical background of affinity chromatography from the beginning of the discipline to the most recent outcomes is first presented. Then the focus is centered on aptamers which represent the last step so far to the long quest for affinity ligands associating very high specificity, availability and strong stability against most harsh cleaning agents required in chromatography. Then technologies of ligand selection from large libraries followed by the most appropriate chemical grafting approaches are described and supported by a number of bibliographic references. Experimental results assembled from relevant published paper are reported; they are selected by their practical applicability and potential use at large scale. The review concludes with specific remarks and future developments that are expected in the near future to turn this technology into a large acceptance for preparative applications.

Aptamers as Valuable Molecular Tools in Neurosciences

Aptamers are short nucleic acids that interact with a variety of targets with high affinity and specificity. They have been shown to inhibit biological functions of cognate target proteins, and they are identifiable by an in vitro selection process, also termed SELEX (Systematic Evolution of Ligands by EXponential enrichment). Being nucleic acids, aptamers can be synthesized chemically or enzymatically. The latter renders RNA aptamers compatible with the cell's own transcription machinery and, thus, expressable inside cells. The synthesis of aptamers by chemical approaches opens up the possibility of producing aptamers on a large scale and enables a straightforward access to introduce modifications in a site-specific manner (e.g., fluorophores or photo-labile groups). These characteristics make aptamers broadly applicable (e.g., as an analytical, diagnostic, or separation tool). In this TechSight, we provide a brief overview on aptamer technology and the potential of aptamers as valuable research tools in neurosciences.

Sequence requirements of oligonucleotide chiral selectors for the capillary electrophoresis resolution of low-affinity DNA binders

We recently reported that a great variety of DNA oligonucleotides (ONs) used as chiral selectors in partial-filling capillary electrophoresis (CE) exhibited interesting enantioresolution properties toward low-affinity DNA binders. Herein, the sequence prerequisites of ONs for the CE enantioseparation process were studied. First, the chiral resolution properties of a series of homopolymeric sequences (Poly-dT) of different lengths (from 5 to 60-mer) were investigated. It was shown that the size increase-dependent random coil-like conformation of Poly-dT favorably acted on the apparent selectivity and resolution. The base-unpairing state constituted also an important factor in the chiral resolution ability of ONs as the switch from the single-stranded to double-stranded structure was responsible for a significant decrease in the analyte selectivity range. Finally, the chemical diversity enhanced the enantioresolution ability of single-stranded ONs. The present work could lay the foundation for the design of performant ON chiral selectors for the CE separation of weak DNA binder enantiomers.

DNA aptamer affinity ligands for highly selective purification of human plasma-related proteins from multiple sources

Nucleic acid aptamers are promising ligands for analytical and preparative-scale affinity chromatography applications. However, a full industrial exploitation requires that aptamer-grafted chromatography media provide a number of high technical standards that remained largely untested. Ideally, they should exhibit relatively high binding capacity associated to a very high degree of specificity. In addition, they must be highly resistant to harsh cleaning/sanitization conditions, as well as to prolonged and repeated exposure to biological environment. Here, we present practical examples of aptamer affinity chromatography for the purification of three human therapeutic proteins from various sources: Factor VII, Factor H and Factor IX. In a single chromatographic step, three DNA aptamer ligands enabled the efficient purification of their target protein, with an unprecedented degree of selectivity (from 0.5% to 98% of purity in one step). Furthermore, these aptamers demonstrated a high stability under harsh sanitization conditions (100h soaking in 1M NaOH). These results pave the way toward a wider adoption of aptamer-based affinity ligands in the industrial-scale purification of not only plasma-derived proteins but also of any other protein in general.

Tunable Supramolecular Interactions of Aggregation-Induced Emission Probe and Graphene Oxide with Biomolecules: An Approach toward Ultrasensitive Label-Free and "Turn-On" DNA Sensing

Aggregation-induced emission (AIE) probes have shown great potential applications in fluorescent sensing of biomolecules, and the integration of AIE probe and graphene oxide (GO) attracts intense interest in developing new tools for label-free and "turn-on" fluorescent biomolecular analysis. Herein, an ultrasensitive label-free and "turn-on" DNA sensing is realized by tuning the supramolecular interactions of AIE probe and GO with DNA. The investigation of supramolecular interactions of AIE probes and GO with DNA demonstrate that AIE probe with short alkyl chains substitute shows highest binding affinity with DNA strand, and GO with low oxidation degree possesses strong binding interactions to ssDNA and the highest fluorescence quenching efficiency. As a result, the optimized AIE probes and GO-based fluorescent sensor can selectively detect the target DNA sequence and exhibits the detection limitation as low as 0.17 × 10^-9 m. It is believed that the research efforts will provide an efficient approach to improve the performance of DNA sensing assay and an indepth understanding of the supramolecular interactions of AIE probes and GO with DNA, and thus facilitate their extended applications in biosensors and biomedicine.

A novel "signal-on/off" sensing platform for selective detection of thrombin based on target-induced ratiometric electrochemical biosensing and bio-bar-coded nanoprobe amplification strategy

A novel dual-signal ratiometric electrochemical aptasensor for highly sensitive and selective detection of thrombin has been designed on the basis of signal-on and signal-off strategy. Ferrocene labeled hairpin probe (Fc-HP), thrombin aptamer and methyl blue labeled bio-bar-coded AuNPs (MB-P3-AuNPs) were rationally introduced for the construction of the assay platform, which combined the advantages of the recognition of aptamer, the amplification of bio-bar-coded nanoprobe, and the ratiometric signaling readout. In the presence of thrombin, the interaction between thrombin and the aptamer leads to the departure of MB-P3-AuNPs from the sensing interface, and the conformation of the single stranded Fc-HP to a hairpin structure to take the Fc confined near the electrode surface. Such conformational changes resulted in the oxidation current of Fc increased and that of MB decreased. Therefore, the recognition event of the target can be dual-signal ratiometric electrochemical readout in both the "signal-off" of MB and the "signal-on" of Fc. The proposed strategy showed a wide linear detection range from 0.003 to 30nM with a detection limit of 1.1 pM. Moreover, it exhibits good performance of excellent selectivity, good stability, and acceptable fabrication reproducibility. By changing the recognition probe, this protocol could be easily expanded into the detection of other targets, showing promising potential applications in disease diagnostics and bioanalysis.

Proximity Binding and Metal Ion-Dependent DNAzyme Cyclic Amplification-Integrated Aptasensor for Label-Free and Sensitive Electrochemical Detection of Thrombin

Thrombin plays important roles for the diagnosis of neurodegenerative and cardiovascular diseases. By integrating proximity binding-induced strand displacement and metal ion-dependent DNAzyme recycling amplification, we demonstrate here the development of a simple and sensitive strategy for the detection of thrombin in human serums. The binding of the two distinct aptamers to the thrombin targets increases the local concentration of the aptamers and facilitates the release of the enzymatic sequences through proximity binding-induced strand displacement. The liberated enzymatic sequences further hybridize with the G-quadruplex containing and hairpin-structured substrate sequences on the sensor electrode to form the metal-ion dependent DNAzymes. Subsequently, the metal ions catalyze the cleavage of the substrate sequences to unlock the G-quadruplex forming sequences and to release the enzymatic sequences to trigger another cleavage cycle. Such metal ion-dependent DNAzyme recycling amplification leads to the formation of many active G-quadruplex forming sequences, which associate with hemin to form G-quadruplex/hemin complexes on the electrode surface. Direct electron transfer of hemin to the electrode during the potential scan can thus generate significantly amplified current for sensitive detection of thrombin at the low picomolar level. The work demonstrated here can thus offer new opportunities for the development of convenient signal amplification strategies for detecting various protein targets.

Molecularly Imprinted Polymers for the Identification and Separation of Chiral Drugs and Biomolecules

Molecularly imprinting polymers (MIPs) have been extensively applied in chromatography for the separation of chiral drugs. In this review, we mainly summarize recent developments of various MIPs used as chiral stationary phases (CSPs) in high performance liquid chromatography (HPLC), capillary electrochromatography (CEC), and supercritical fluid chromatography (SFC). Among them, HPLC has the advantages of straightforward operation and high selectivity. However, the low separation efficiency, due to slow interaction kinetics and heavy peak broadening, is the main challenge for the application of MIPs in HPLC. On the other hand, CEC possesses both the high selectivity of HPLC and the high efficiency of capillary electrophoresis. In CEC, electroosmotic flow is formed across the entire column and reduces the heavy peak broadening observed in HPLC mode. SFC can modify the low interaction kinetics in HPLC when supercritical fluids are utilized as mobile phases. If SFC and MIP-based CSPs can be well combined, better separation performance can be achieved. Particles, monoliths and membrane are typical formats of MIPs. Traditional MIP particles produced by bulk polymerization have been replaced by MIP particles by surface imprinting technology, which are highly consistent in size and shape. Monolithic MIPs are prepared by in situ method in a column, greatly shortening the pre-preparation time. Some novel materials, such as magnetic nanoparticles, are integrated into the MIPs to enhance the controllability and efficiency of the polymerization. This review will be helpful to guide the preparation, development, and application of MIPs in chromatographic and electrophoretic enantioseparation.

In vitro selection of antibiotic-binding aptamers

Despite its wide applicability the selection of small molecule-binding RNA aptamers with high affinity binding and specificity is still challenging. We will present here a protocol which allows the in vitro selection of antibiotic-binding aptamers which turned out to be important building blocks for the design process of synthetic riboswitches. The presented methods will be compared with alternative in vitro selection protocols. A detailed note section will point out useful tips and pitfalls.

Taurine Boosts Cellular Uptake of Small D-Peptides for Enzyme-Instructed Intracellular Molecular Self-Assembly

Due to their biostability, D-peptides are emerging as an important molecular platform for biomedical applications. Being proteolytically resistant, D-peptides lack interactions with endogenous transporters and hardly enter cells. Here we show that taurine, a natural amino acid, drastically boosts the cellular uptake of small D-peptides in mammalian cells by >10-fold, from 118 μM (without conjugating taurine) to >1.6 mM (after conjugating taurine). The uptake of a large amount of the ester conjugate of taurine and D-peptide allows intracellular esterase to trigger intracellular self-assembly of the D-peptide derivative, further enhancing their cellular accumulation. The study on the mechanism of the uptake reveals that the conjugates enter cells via both dynamin-dependent endocytosis and macropinocytosis, but likely not relying on taurine transporters. Differing fundamentally from the positively charged cell-penetrating peptides, the biocompatibility, stability, and simplicity of the enzyme-cleavable taurine motif promise new ways to promote the uptake of bioactive molecules for countering the action of efflux pump and contributing to intracellular molecular self-assembly.

Chiral resolution capabilities of DNA oligonucleotides

Herein, we studied the chiral resolution properties of a repertoire of arbitrarily chosen DNA oligonucleotides (ON). Ten oligonucleotidic sequences characterized by diverse base compositions, sizes, and structural features, ranging from secondary structure-free homo-oligonucleotides to duplex, hairpin, and three-way junction architectures, were investigated as potential chiral selectors. Their enantioselective features were assessed by using ONs as running buffer additives in partial-filling capillary electrophoresis. It was shown that all the screened sequences displayed enantiodiscrimination capabilities toward small aromatic compounds. Under (sub)millimolar DNA concentration conditions, the combination of only three oligonucleotidic sequences provided the chiral resolution of around 20 racemates, including drugs, illegal drugs, amino-acids, and nucleosides. This work represents the first demonstration of such analyte selectivity spectrum for nucleic acid-based chiral separation tools.

Bi-functionalized aptasensor for ultrasensitive detection of thrombin

A novel bi-functionalized aptasensor for thrombin detection was fabricated by using electrochemiluminescence (ECL) and electrochemical impedance spectroscopy (EIS) techniques. A thiol-terminated aptamer with 15 oligonucleotides was hybridized with its complementary oligonucleotides to form a double-stranded DNA (dsDNA). Then, the thiol-labeled dsDNA was assembled on a Au electrode via Au-S bond; the other distal of the dsDNA labeled with biotin was bound to QDs through a biotin-avidin conjugation. When thrombin is present in the detection solution, the aptamer can combine with thrombin, resulting in loss of CdSe QDs from the electrode surface and thereby decreasing the ECL intensity and increasing the impedance. The decreased ECL and increased EIS signals are logarithmically linear with respect to the concentration of thrombin. The linear range was 10(-10)-10(-3) μg mL(-1) (R=0.9924) for the ECL signal and 10(-10)-10(-1) μg mL(-1) (R=0.9875) for the EIS method with a common detection limit of 10(-10) μg mL(-1) (2.7 aM). In addition, the bi-functionalized aptasensor exhibited excellent selectivity, super sensitivity, a low detection limit and a wide linear range.

A novel label-free aptasensor based on target-induced structure switching of aptamer-functionalized mesoporous silica nanoparticles

A strategy for high-performance liquid chromatography detection of adenosine triphosphate was developed based on mesoporous silica nanoparticles functionalized with an aptamer as a cap.

Polymerization of affinity ligands on a surface for enhanced ligand display and cell binding

Surfaces functionalized with affinity ligands have been widely studied for applications such as biological separations and cell regulation. While individual ligands can be directly conjugated onto a surface, it is often important to conjugate polyvalent ligands onto the surface to enhance ligand display. This study was aimed at exploring a method for surface functionalization via polymerization of affinity ligands, which was achieved through ligand hybridization with DNA polymers protruding from the surface. The surface with polyvalent ligands was evaluated via aptamer-mediated cell binding. The results show that this surface bound target cells more effectively than a surface directly functionalized with individual ligands in situations with either equal amounts of ligand display or equal amounts of surface reaction sites. Therefore, this study has demonstrated a new strategy for surface functionalization to enhance ligand display and cell binding. This strategy may find broad applications in settings where surface area is limited or the surface of a material does not possess sufficient reaction sites.

Miniaturized DNA aptamer-based monolithic sorbent for selective extraction of a target analyte coupled on-line to nanoLC

A complete characterization of a novel target-specific DNA aptamer-based miniaturized solid phase extraction (SPE)-sorbent coupled on-line to nanoLC is presented. A miniaturized oligosorbent (mOS) was prepared via the in situ sol-gel synthesis of a hybrid organic-inorganic monolith in 100 μm i.d. capillary columns using tetraethoxysilane and 3-aminopropyltriethoxysilane as precursors, followed by covalent binding of a 5'-amino-modified DNA aptamer with a C12 spacer arm specific for a molecule of small molecular weight. Ochratoxin A (OTA), one of the most abundant naturally occurring mycotoxins, was chosen as model analyte to demonstrate the principle of such an approach. The mOS was coupled on-line to RP-nanoLC-LIF. Selective extraction of OTA on several mOSs was demonstrated with an average extraction recovery above 80 % when percolating spiked binding buffer and a low recovery on control monoliths grafted with a non-specific aptamer. Reproducibility of mOSs preparation was highlighted by comparing extraction yields. Otherwise, the mOSs demonstrated no cross-reactivity towards an OTA structural analogue, i.e., ochratoxin B. Due to the high specific surface area of the hybrid silica-based monolith, the coverage density of DNA aptamers covalently immobilized in the capillaries was very high and reached 6.27 nmol μL(-1), thus leading to a capacity above 5 ng of OTA. This miniaturized device was then applied to the selective extraction of OTA from beer samples. It revealed to be effective in isolating OTA from this complex matrix, thus improving the reliability of its analysis at the trace level.

Aptamer-based-sorbents for sample treatment--a review

To improve selectivity during sample pretreatment, various selective tools inducing a molecular recognition mechanism during the extraction procedure have been developed, such as sorbents constituted of immobilized antibodies, i.e., immunosorbents, or molecularly imprinted polymers. More recently, as an alternative to both previous approaches, aptamers immobilized onto a solid support, i.e., oligosorbents, were proposed. Thanks to the high affinity and high selectivity of the interaction that some aptamers offer toward some target analytes, they also provide powerful techniques that make selective extraction and the concentration of a target analyte from liquid matrices in one step or sample purification of extracts from solid matrices possible. This review describes the development and the properties of these oligosorbents developed for different types of targets-pharmaceuticals, mycotoxins, proteins, cells, etc. After describing the immobilization procedures, we discuss different parameters characterizing the potential of aptamer-based supports as extraction sorbents. Close relations exist between extraction recoveries and the affinity and amounts of aptamers immobilized on the extraction device. In addition, analyte-aptamer interactions may be affected by matrix components and by additives in the samples. This may also lower extraction recoveries and affect the stability and the possible reusability of the aptamer-based sorbent. All these points are discussed and illustrated. Numerous examples of applications of these sorbents to the treatment of complex samples such as food samples, environmental samples, and biological fluids are also reported. Their association with analytical devices, from conventional to miniaturized analytical systems, is also discussed.

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.