A rational approach to minimal high-resolution cross-reactive arrays

Exploring the Landscape of Aptamers: From Cross-Reactive to Selective to Specific, High-Affinity Receptors for Cocaine

We reported over 20 years ago MNS-4.1, the first DNA aptamer with a micromolar affinity for cocaine. MNS-4.1 is based on a structural motif that is very common in any random pool of oligonucleotides, and it is actually a nonspecific hydrophobic receptor with wide cross-reactivity with alkaloids and steroids. Despite such weaknesses preventing broad applications, this aptamer became widely used in proof-of-concept demonstrations of new formats of biosensors. We now report a series of progressively improved DNA aptamers recognizing cocaine, with the final optimized receptors having low nanomolar affinity and over a thousand-fold selectivity over the initial cross-reactants. In the process of optimization, we tested different methods to eliminate cross-reactivities and improve affinity, eventually achieving properties that are comparable to those of the reported monoclonal antibody candidates for the therapy of overdose. Multiple aptamers that we now report share structural motifs with the previously reported receptor for serotonin. Further mutagenesis studies revealed a palindromic, highly adaptable, broadly cross-reactive hydrophobic motif that could be rebuilt through mutagenesis, expansion of linker regions, and selections into receptors with exceptional affinities and varying specificities.

Aggregation-Induced Emission Molecule Microwire-Based Specific Organic Vapor Detector through Structural Modification

An optical organic vapor sensor array based on colorimetric or fluorescence changes quantified by spectroscopy provides an efficient method for realizing rapid identification and detection of organic vapor, but improving the sensitivity of the optical organic vapor sensor is challenging. Here, AIE/polymer (AIE, ggregation-induced emission) composites into microwires arrays are fabricated as organic vapor sensors with specific recognition and high sensitivity for different vapors using the capillary-bridge-mediated assembly method. Such organic vapor sensor successfully detects organic vapor relying on a swelling-induced fluorescence change of the AIE/polymer composites, combating the unique property of AIE molecules and vapor absorption-induced polymer swelling. A series of AIE/polymer composites into microwires arrays with four different groups on the AIE molecule and four different side chains on the polymer is fabricated to detect four different organic vapors. The mechanism for improved sensitivity of the AIE/polymer composites microwires arrays sensors is the same because of the similar polarity between the group of AIE molecules and the vapor molecules. Molecular design of the side chains of the polymer and the groups of AIE molecules based on the polarity of the targeted vapor molecule can enhance the sensitivity of the sensors to the subparts per million level.

Ordered-Assembly Conductive Nanowires Array with Tunable Polymeric Structure for Specific Organic Vapor Detection

An artificial organic vapor sensor based on a finite number of 1D nanowires arrays can provide a strategy to allow classification and identification of different analytes with high efficiency, but fabricating a 1D nanowires array is challenging. Here, a coaxial Ag/polymer nanowires array is prepared as an organic vapor sensor with specific recognition, using a strategy combining superwettability-based nanofabrication and polymeric swelling-induced resistance change. Such organic vapor sensor containing commercial polymers can successfully classify and identify various organic vapors with good separation efficiency. An Ag/polymer nanowires array with synthetic polyethersulfone polymers is also fabricated, through molecular structure modification of the polymers, to distinguish the similar organic vapors of methanol and ethanol. Theoretical simulation results demonstrate introduction of specific molecular interaction between the designed polymers and organic vapors can improve the specific recognition performance of the sensors.

Fluorescence detection of single-nucleotide differences using aptamer-forming binary DNA probes

We report a simple method for fluorescence detection of single-nucleotide alterations in a long target DNA, which is based on the formation of a three-way-junction-structured cholic-acid-binding DNA aptamer by the hybridization of the target with binary DNA probes. The new method was successfully exploited for SNP genotyping of human CYP2C19 gene.

Highly-sensitive optical organic vapor sensor through polymeric swelling induced variation of fluorescent intensity

Traditional optical organic vapor sensors with solvatochromic shift mechanisms have lower sensitivity due to weak intermolecular interactions. Here, we report a general strategy to prepare a higher sensitivity optical organic vapor sensor through polymeric swelling-induced variation of fluorescent intensity. We combine one-dimensional polymeric structures and aggregation-induced emission (AIE) molecules together to form a polymer/AIE microwires array as a sensor. The prepared sensors based on different commercial polymers can successfully classify and identify various organic vapors. Among them, the poly(vinyl butyral)/AIE microwires array can detect methanol vapor as low as 0.05% of its saturation vapor pressure. According to the theory of like dissolves like, we further fabricate a polymer/AIE microwires array derived from designable polyethersulfones, through regulating their side chains, to distinguish similar organic vapors of benzene and toluene. Both experimental and theoretical simulation results reveal that specific molecular interactions between the polyethersulfones and organic vapors can improve the specific recognition performance of the sensors.

A colorimetric sensor array based on sulfuric acid assisted KMnO4 fading for the detection and identification of pesticides

Pesticides play a critical role in improving crop yield in modern agriculture, but their residues significantly harm the environment and human health. Herein, a novel and simple colorimetric sensor array built on sulfuric acid assisted KMnO₄ fading strategy has been developed for pesticides detection and discrimination. This sensor array is facilely fabricated by KMnO₄ and sulfuric acid through simply adjusting their concentrations and ratios. Hierarchical clustering analysis (HCA) demonstrates that the as-fabricated colorimetric sensor array has a high dimensionality, and shows excellent capability to recognize common kinds of pesticides from potential interferants. Semi-quantitative detection was achieved through combining HCA and corresponding fitting curves. Moreover, the proposed sensor array was successfully applied to detect pesticide residues (e.g. carbaryl) in real samples. The strategy described herein will not only "maximally" simplify the design and fabrication approach, but expand the application fields of colorimetric sensor array methodology towards weak-reactive analytes.

High-Affinity Nucleic-Acid-Based Receptors for Steroids

Artificial receptors for hydrophobic molecules usually have moderate affinities and limited selectivities. We describe three new classes of high affinity hydrophobic receptors for nonaromatic steroids based on deoxyribonucleotides, obtained through five high stringency selections coupled with tailored counter-selections. The isolation of multiple classes of high affinity steroid receptors demonstrates the surprising breadth of moderately sized hydrophobic binding motifs (<40 nucleotides) available to natural nucleic acids. Studies of interactions with analogs indicate that two classes, four-way junctions and 4XG_N motifs, comprise receptors with shapes that prevent binding of specific steroid conjugates used in counter-selections. Furthermore, they strongly prefer nonhydroxylated steroid cores, which is typical for hydrophobic receptors. The third new class accommodates hydroxyl groups in high-affinity, high-selectivity binding pockets, thus reversing the preferences of the first two classes. The high-affinity binding of aptamers to targets efficiently inhibits double-helix formation in the presence of the complementary oligonucleotides. The high affinity of some of these receptors and tailored elimination of binding through counter-selections ensures that these new aptamers will enable clinical chemistry applications.

AIE-doped poly(ionic liquid) photonic spheres: a single sphere-based customizable sensing platform for the discrimination of multi-analytes

By simultaneously exploiting the unique properties of ionic liquids and aggregation-induced emission (AIE) luminogens, as well as photonic structures, a novel customizable sensing system for multi-analytes was developed based on a single AIE-doped poly(ionic liquid) photonic sphere. It was found that due to the extraordinary multiple intermolecular interactions involved in the ionic liquid units, one single sphere could differentially interact with broader classes of analytes, thus generating response patterns with remarkable diversity. Moreover, the optical properties of both the AIE luminogen and photonic structure integrated in the poly(ionic liquid) sphere provide multidimensional signal channels for transducing the involved recognition process in a complementary manner and the acquisition of abundant and sufficient sensing information could be easily achieved on only one sphere sensor element. More importantly, the sensing performance of our poly(ionic liquid) photonic sphere is designable and customizable through a simple ion-exchange reaction and target-oriented multi-analyte sensing can be conveniently realized using a selective receptor species, such as counterions, showing great flexibility and extendibility. The power of our single sphere-based customizable sensing system was exemplified by the successful on-demand detection and discrimination of four multi-analyte challenge systems: all 20 natural amino acids, nine important phosphate derivatives, ten metal ions and three pairs of enantiomers. To further demonstrate the potential of our spheres for real-life application, 20 amino acids in human urine and their 26 unprecedented complex mixtures were also discriminated between by the single sphere-based array.

Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer

Using NMR magnetization transfer experiments, the hydrogen exchange rate constants (k _ex ) of the DNA imino protons in the cocaine-binding aptamer have been determined for the free, cocaine-bound, and quinine-bound states. The secondary structure of the cocaine-binding aptamer is composed of three stems built around a three-way junction. In the free aptamer the slowest exchanging imino protons are located in the middle of the stems. The highest k _ex values were found for a nucleotide in the GAA loop of stem 3 and for nucleotides at the end of the stems that form the three-way junction structure and in the tandem GA mismatch. Upon ligand binding, the k _ex values of nucleotides at the ligand binding site are reduced, indicating that these base pairs become more stable or less solvent accessible in the bound state. The imino proton k _ex values of nucleotides located away from the binding site are only minimally affected by ligand binding.

Modulating the Substrate Selectivity of DNA Aptamers Using Surfactants

Nucleic acid aptamers have a number of advantages compared to antibodies, including greater ease of production and increased thermal stability. We hypothesized that aptamers may also be capable of functioning in the presence of high concentrations of surfactants, which readily denature antibodies and other protein-based affinity reagents. Here we report the first systematic investigation into the compatibility of DNA aptamers with surfactants. We find that neutral and anionic surfactants have only a minor impact on the ability of aptamers to fold and bind hydrophilic target molecules. Additionally, we demonstrate that surfactants can be utilized to modulate the substrate binding preferences of aptamers, likely due to the sequestration of hydrophobic target molecules within micelles. The compatibility of aptamers with commonly used surfactants is anticipated to expand their scope of potential applications, and the ability to modulate the substrate binding preferences of aptamers using a simple additive provides a novel route to increasing their selectivity in analytical applications.

Structure-affinity relationship of the cocaine-binding aptamer with quinine derivatives

In addition to binding its target molecule, cocaine, the cocaine-binding aptamer tightly binds the alkaloid quinine. In order to understand better how the cocaine-binding aptamer interacts with quinine we have used isothermal titration calorimetry-based binding experiments to study the interaction of the cocaine-binding aptamer to a series of structural analogs of quinine. As a basis for comparison we also investigated the binding of the cocaine-binding aptamer to a set of cocaine metabolites. The bicyclic aromatic ring on quinine is essential for tight affinity by the cocaine-binding aptamer with 6-methoxyquinoline alone being sufficient for tight binding while the aliphatic portion of quinine, quinuclidine, does not show detectable binding. Compounds with three fused aromatic rings are not bound by the aptamer. Having a methoxy group at the 6-position of the bicyclic ring is important for binding as substituting it with a hydrogen, an alcohol or an amino group all result in lower binding affinity. For all ligands that bind, association is driven by a negative enthalpy compensated by unfavorable binding entropy.

A differential fluorescent receptor for nucleic acid analysis

Differential receptors use an array of sensors to recognize analytes. Each sensor in the array can recognize not one, but several analytes with different rates, so a single analyte triggers a response of several sensors in the array. The receptor thus produces a pattern of signals that is unique for each analyte, thereby enabling identification of a specific analyte by producing a "fingerprint" pattern. We applied this approach for the analysis of DNA sequences of Mycobacterium tuberculosis strains that differ by single nucleotide substitutions in the 81-bp hot-spot region that imparts rifampin resistance. The technology takes advantage of the new multicomponent, selfassembling sensor, which produces a fluorescent signal in the presence of specific DNA sequences. A differential fluorescent receptor (DFR) contained an array of three such sensors and differentiated at least eight DNA sequences. The approach requires only one molecular-beacon-like fluorescent reporter, which can be used by all three sensors. The DFR developed in this study represents a cost-efficient alternative to molecular diagnostic technologies that use fluorescent hybridization probes.

A graphene-based sensor array for high-precision and adaptive target identification with ensemble aptamers

In this work, we report a new concept of adaptive "ensemble aptamers" (ENSaptamers) that exploits the collective recognition abilities of a small set of rationally designed, nonspecific DNA sequences to identify molecular or cellular targets discriminatively. In contrast to in vitro-selected aptamers, which possess specific "lock-and-key" recognition, ENSaptamers rely on pattern recognition that mimics natural olfactory or gustatory systems. Nanographene oxide was employed to provide a low-background and highly reproducible fluorescent assay system. We demonstrate that this platform provides a highly discriminative and adaptive tool for high-precision identification of a wide range of targets for diagnostic and proteomic applications with a nearly unlimited supply of ENSaptamer receptors.

Optimizing cross-reactivity with evolutionary search for sensors

We report a straightforward evolutionary procedure to build an optimal sensor array from a pool of DNA sequences oriented toward three-way junctions. The individual sensors were mined from this pool under separate selection pressures to interact with four steroids, while allowing cross-reactivity, in a manner designed to achieve perfect classification of individual steroids. The resulting sensor array had three sensors and displayed discriminatory capacity between steroid classes over full ranges of concentrations. We propose that similar protocols can be used whenever we have two or more classes of samples, with individual classes being defined through gross differences in ratios of dominant families of responsive components.

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.

Aptamer-mediated surface-enhanced Raman spectroscopy intensity amplification

A bifunctional adenosine-sensitive double-stranded DNA aptamer was used to create and control a surface-enhanced Raman spectroscopy (SERS) hot spot between a bulk Au surface and a gold nanoparticle (Au NP) attached to the aptamer via a biotin-avidin linkage. The Au NP was decorated with 4-aminobenzenethiol (4-ABT), a Raman reporter molecule. In the presence of adenosine, the target molecule, the SERS spectrum of 4-ABT increased in intensity by (concentration-dependent) factors as large as ∼4; in situ, atomic force microscopy imaging showed the mean height of the Au NP-bearing aptamer to decrease by ∼5 nm consistent with the observed SERS intensity change. Because the aptamer's geometrical change is induced by one or two molecules, while the resulting SERS intensity changes involve many reporter molecules residing in the modified hot spot, the aptamer amplifies the SERS effect.

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.

Detecting hydrophobic molecules with nucleic acid-based receptors

We will argue for applications of crossreactive arrays of solution-phase sensors in urinalysis, wherein these can be useful for screening, as well as monitoring of disease progress or treatment compliance. For our first demonstration we focus on the detection and classification process of the predominant hydrophobic molecules in urine, steroids, while taking advantage of a variety of differentially crossreactive DNA-based hydrophobic receptors, three-way junctions. We discuss our progress in addressing some of the traditional limitations of crossreactive arrays and what remains to be done to move these systems into clinical applications.

High-resolution cross-reactive array for alkaloids

A high-resolution cross-reactive array capable of classifying alkaloids over a range of concentrations was generated by systematic introduction of a nitroindole analog into a hydrophobic pocket within a DNA three-way junction to match structural motifs presented by the analytes.

Recognition of phospho sugars and nucleotides with an array of boronic acid appended bipyridinium salts

The solution-phase sensor array of three cationic bis-boronic acid appended benzyl viologens (BBV) and the anionic fluorescent dye, 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS), is able to discriminate among five phospho sugars, four nucleotides and three neutral saccharides in aqueous buffered solution at low mM concentrations. Linear discriminant analysis, principal component analysis, and hierachical cluster analysis studies showed the "discrimination limit" (lowest analyte concentration where the discrimination is still 100%) to be 4mM. Calculated K(b) and F(max)/F(0) values from binding curves of the three BBVs with 1-12 were also used to perform multi-variate analyses with very good discrimination results.