DNA nanotechnology for nucleic acid analysis: sensing of nucleic acids with DNA junction-probes.

DNA nanotechnology deals with the design of non-naturally occurring DNA nanostructures that can be used in biotechnology, medicine, and diagnostics. In this study, we introduced a nucleic acid five-way junction (5WJ) structure for direct electrochemical analysis of full-length biological RNAs. To the best of our knowledge, this is the first report on the interrogation of such long nucleic acid sequences by hybridization probes attached to a solid support. A hairpin-shaped electrode-bound oligonucleotide hybridizes with three adaptor strands, one of which is labeled with methylene blue (MB). The four strands are combined into a 5WJ structure only in the presence of specific DNA or RNA analytes. Upon interrogation of a full-size 16S rRNA in the total RNA sample, the electrode-bound MB-labeled 5WJ association produces a higher signal-to-noise ratio than electrochemical nucleic acid biosensors of alternative design. This advantage was attributed to the favorable geometry on the 5WJ nanostructure formed on the electrode's surface. The 5WJ biosensor is a cost-efficient alternative to the traditional electrochemical biosensors for the analysis of nucleic acids due to the universal nature of both the electrode-bound and MB-labeled DNA components.

Cost-Effective Modular Biosensor for SARS-CoV-2 and Influenza A Detection.

A modular, multi-purpose, and cost-effective electrochemical biosensor based on a five-stranded four-way junction (5S-4WJ) system was developed for SARS-CoV-2 (genes S and N) and Influenza A virus (gene M) detection. The 5S-4WJ structure consists of an electrode-immobilized universal stem-loop (USL) strand, two auxiliary DNA strands, and a universal methylene blue redox strand (UMeB). This design allows for the detection of specific nucleic acid sequences using square wave voltammetry (SWV). The sequence-specific auxiliary DNA strands (m and f) ensure selectivity of the biosensor for target recognition utilizing the same USL and UMeB components. An important feature of this biosensor is the ability to reuse the USL-modified electrodes to detect the same or alternative targets in new samples. This is accomplished by a simple procedure involving rinsing the electrodes with water to disrupt the 5S-4WJ structure and subsequent re-hybridization of the USL strand with the appropriate set of strands for a new analysis. The biosensor exhibited minimal loss in signal after rehybridization, demonstrating its potential as a viable multiplex assay for both current and future pathogens, with a low limit of quantification (LOQ) of as low as 17 pM.

Single-Step Integration of Poly(3-Octylthiophene) and Single-Walled Carbon Nanotubes for Highly Reproducible Paper-Based Ion-Selective Electrodes.

Calibration of ion-selective electrodes (ISEs) is cumbersome, time-consuming, and constitutes a significant limitation for the development of single-use and wearable disposable sensors. To address this problem, we have studied the effect of ion-selective membrane solvent on ISE reproducibility by comparing tetrahydrofuran (THF) (a typical solvent for membrane preparation) and cyclohexanone. In addition, a single-step integration of semiconducting/transducer polymer poly(3-octylthiophene) (POT) with single-walled carbon nanotubes (SWCNTs) into the paper-based ISEs (PBISEs) substrate was introduced. PBISEs for potassium and sodium ions were developed, and these ISEs present outstanding sensor performance and high potential reproducibility, as low as ±1.0 mV (n = 3).

Selective Determination of Isothermally Amplified Zika Virus RNA Using a Universal DNA-Hairpin Probe in Less than 1 Hour.

The recent outbreak of the Zika virus (ZIKV) in the Americas and multiple studies that linked the virus to the cases of microcephaly and neurological complications have revealed the need for cost efficient and rapid ZIKV diagnostics tests. Here, a diagnostic platform relying on a four-way junction (4WJ)-based biosensor with electrochemical readout using a Universal DNA-Hairpin (UDH) probe for the selective recognition of an isothermally amplified ZIKV RNA fragment is developed. The 4WJ structure utilizes an electrode-immobilized stem-loop (DNA-hairpin) probe and two DNA adaptor strands complementary to both the stem-loop probe and the targeted fragment of a ZIKV amplicon. One of the adaptor strands is responsible for high selectivity of the target recognition, while another helps unwinding the target secondary structure. The first adaptor strand contains a redox label methylene blue to trigger the current change in response to the target-dependent formation of the 4WJ structure on the surface of the electrode. The amplicon can be analyzed directly from the amplification sample without the need for its purification. The proposed diagnostic methodology exhibits the limit of ZIKV RNA detection of 1.11 fg/µL (∼0.3 fM) and high selectivity that allows for reliable discrimination of ZIKV from West Nile virus and four dengue virus serotypes. Overall, the analysis of ZIKV RNA can be completed in less than 1 h, including amplification and electrochemical detection.

A universal and label-free impedimetric biosensing platform for discrimination of single nucleotide substitutions in long nucleic acid strands.

We report a label-free universal biosensing platform for highly selective detection of long nucleic acid strands. The sensor consists of an electrode-immobilized universal stem-loop (USL) probe and two adaptor strands that form a 4J structure in the presence of a specific DNA/RNA analyte. The sensor was characterized by electrochemical impedance spectroscopy (EIS) using K3[Fe(CN)6]/K4[Fe(CN)6] redox couple in solution. An increase in charge transfer resistance (RCT) was observed upon 4J structure formation, the value of which depends on the analyte length. Cyclic voltammetry (CV) was used to further characterize the sensor and monitor the electrochemical reaction in conjunction with thickness measurements of the mixed DNA monolayer obtained using spectroscopic ellipsometry. In addition, the electron transfer was calculated at the electrode/electrolyte interface using a rotating disk electrode. Limits of detection in the femtomolar range were achieved for nucleic acid targets of different lengths (22 nt, 60 nt, 200 nt). The sensor produced only a background signal in the presence of single base mismatched analytes, even in hundred times excess in concentration. This label-free and highly selective biosensing platform is versatile and can be used for universal detection of nucleic acids of varied lengths which could revolutionize point of care diagnostics for applications such as bacterial or cancer screening.

A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences.

Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode's surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode's surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets.

Circumventing Traditional Conditioning Protocols in Polymer Membrane-Based Ion-Selective Electrodes.

Preparation of ion-selective electrodes (ISEs) often requires long and complicated conditioning protocols limiting their application as tools for in-field measurements. Herein, we eliminated the need for electrode conditioning by loading the membrane cocktail directly with primary ion solution. This proof of concept experiment was performed with iodide, silver, and sodium selective electrodes. The proposed methodology significantly shortened the preparation time of ISEs, yielding functional electrodes with submicromolar detection limits. Moreover, it is anticipated that this approach may form the basis for the development of miniaturized all-solid-state ion-selective electrodes for in situ measurements.

Nanomolar detection limits of Cd²âº, Ag⁺, and K⁺ using paper-strip ion-selective electrodes.

Paper-based ion-selective electrodes (ISEs) are simple, flexible, and cost-efficient in comparison to conventional solid-contact ISEs. Yet, paper-based ISEs have poor limits of detection (in the micromolar range) relative to conventional solid-contact ISEs. Here we describe the construction and optimization of ISEs based on commercially available filter paper modified with single-walled carbon nanotubes (SWCNTs), sputtered gold, and conductive polymer poly(3-octylthiophene) to support an ion-selective membrane. The ion-selective membrane presented here is based on the copolymer methyl methacrylate-decyl methacrylate (MMA-DMA). The copolymer MMA-DMA is highly water-repellent and has a low coefficient of diffusion, which makes it particularly suitable for the creation of sensors with high performance in reaching low limits of detection. Three different configurations of the electrodes have been characterized by using contact angle surface analysis, oxygen influence, and testing for the presence of a water layer. Paper-strip ISEs for cadmium, silver, and potassium ions were developed with groundbreaking limits of detection of 1.2, 25.1, and 11.0 nM, respectively. In addition to such low limits of detection, paper-strip ISEs display high selectivity for their ion of interest and high reproducibility.

Visible light activated ion sensing using a photoacid polymer for calcium detection.

Presented here is a sensing membrane consisting of a modified merocyanine photoacid polymer and a calcium ionophore in plasticized poly(vinyl chloride). This membrane is shown to actively exchange protons with calcium ions when switched ON after illumination at 470 nm, and the exchange can be followed by UV-vis spectroscopy. The sensing membrane shows no response in the ON state when calcium ions are absent. The limit of detection of the sensor is 5.0 × 10(-4) M with an upper detection limit of 1.0 M. Thus, we demonstrate for the first time the use of a visible light activated, lipophilic photoacid polymer in an ion-sensing membrane for calcium ions, which highly discriminates potassium, sodium, and magnesium ions.

Manipulating Mechanical Properties with Electricity: Electroplastic Elastomer Hydrogels.

The dawn of the 21st century has brought with it an increasing interest in emulating the adaptive finesse of natural systems by designing materials with on-demand, tunable properties. The creation of such responsive systems could be expected, based on historical precedent, to lead to completely new engineering design paradigms. Using a bioinspired approach of coupling multiple equilibria that operate on different length scales, a material whose bulk mechanical properties can be manipulated by electrical input has been developed. The new macroscale electroplastic elastomer hydrogels can be reversibly cycled through soft and hard states while maintaining a three-dimensional shape by sequential application of oxidative and reductive potentials. This input changes the cross-linking capacity of iron ions within the gel matrix, between a poorly coordinating +2 and a more strongly binding +3 oxidation state. Inclusion of carbon nanotubes in the hydrogel preparation increases conductivity and decreases transition time.

A comparative study of enzyme immobilization strategies for multi-walled carbon nanotube glucose biosensors.

This work addresses the comparison of different strategies for improving biosensor performance using nanomaterials. Glucose biosensors based on commonly applied enzyme immobilization approaches, including sol-gel encapsulation approaches and glutaraldehyde cross-linking strategies, were studied in the presence and absence of multi-walled carbon nanotubes (MWNTs). Although direct comparison of design parameters such as linear range and sensitivity is intuitive, this comparison alone is not an accurate indicator of biosensor efficacy, due to the wide range of electrodes and nanomaterials available for use in current biosensor designs. We proposed a comparative protocol which considers both the active area available for transduction following nanomaterial deposition and the sensitivity. Based on the protocol, when no nanomaterials were involved, TEOS/GOx biosensors exhibited the highest efficacy, followed by BSA/GA/GOx and TMOS/GOx biosensors. A novel biosensor containing carboxylated MWNTs modified with glucose oxidase and an overlying TMOS layer demonstrated optimum efficacy in terms of enhanced current density (18.3 ± 0.5 µA mM(-1) cm(-2)), linear range (0.0037-12 mM), detection limit (3.7 µM), coefficient of variation (2%), response time (less than 8 s), and stability/selectivity/reproducibility. H(2)O(2) response tests demonstrated that the most possible reason for the performance enhancement was an increased enzyme loading. This design is an excellent platform for versatile biosensing applications.

Non-invasive quantification of endogenous root auxin transport using an integrated flux microsensor technique.

Indole-3-acetic acid (IAA) is a primary phytohormone that regulates multiple aspects of plant development. Because polar transport of IAA is an essential determinant of organogenesis and dynamic tropic growth, methods to monitor IAA movement in vivo are in demand. A self-referencing electrochemical microsensor was optimized to non-invasively measure endogenous IAA flux near the surface of Zea mays roots without the addition of exogenous IAA. Enhanced sensor surface modification, decoupling of acquired signals, and integrated flux analyses were combined to provide direct, real time quantification of endogenous IAA movement in B73 maize inbred and brachytic2 (br2) auxin transport mutant roots. BR2 is localized in epidermal and hypodermal tissues at the root apex. br2 roots exhibit reduced shootward IAA transport at the root apex in radiotracer experiments and reduced gravitropic growth. IAA flux data indicates that maximal transport occurs in the distal elongation zone of maize roots, and net transport in/out of br2 roots was decreased compared to B73. Integration of short term real time flux data in this zone revealed oscillatory patterns, with B73 exhibiting shorter oscillatory periods and greater amplitude than br2. IAA efflux and influx were inhibited using 1-N-naphthylphthalamic acid (NPA), and 2-naphthoxyacetic acid (NOA), respectively. A simple harmonic oscillation model of these data produced a correlation between modeled and measured values of 0.70 for B73 and 0.69 for br2. These results indicate that this technique is useful for real-time IAA transport monitoring in surface tissues and that this approach can be performed simultaneously with current live imaging techniques.

Propulsion of nanowire diodes.

The propulsion of semiconductor diode nanowires under external AC electric field is described. Such fuel-free electric field-induced nanowire propulsion offers considerable promise for diverse technological applications.

High-temperature potentiometry: modulated response of ion-selective electrodes during heat pulses.

The concept of locally heated polymeric membrane potentiometric sensors is introduced here for the first time. This is accomplished in an all solid state sensor configuration, utilizing poly(3-octylthiophene) as the intermediate layer between the ion-selective membrane and underlying substrate that integrates the heating circuitry. Temperature pulse potentiometry (TPP) gives convenient peak-shaped analytical signals and affords an additional dimension with these sensors. Numerous advances are envisioned that will benefit the field. The heating step is shown to give an increase in the slope of the copper-selective electrode from 31 to 43 mV per 10-fold activity change, with a reproducibility of the heated potential pulses of 1% at 10 microM copper levels and a potential drift of 0.2 mV/h. Importantly, the magnitude of the potential pulse upon heating the electrode changes as a function of the copper activity, suggesting an attractive way for differential measurement of these devices. The heat pulse is also shown to decrease the detection limit by half an order of magnitude.

Chemical sensing based on catalytic nanomotors: motion-based detection of trace silver.

A motion-based chemical sensing involving fuel-driven nanomotors is demonstrated. The new protocol relies on the use of an optical microscope for tracking changes in the speed of nanowire motors in the presence of the target analyte. Selective and sensitive measurements of trace silver ions are illustrated based on the dramatic and specific acceleration of bimetal nanowire motors in the presence of silver. Such nanomotor-based measurements would lead to a wide range of novel and powerful chemical and biological sensing protocols.

Electrochemically-triggered motion of catalytic nanomotors.

An electrochemically-controlled movement of catalytic nanomotors, including a cyclic 'on/off' activation of the nanomotor motion and a fine speed control, is illustrated.

Thermal modulation of nanomotor movement.

Motion control is essential for various applications of man-made nanomachines. The ability to control and regulate the movement of catalytic nanowire motors is illustrated by applying short heat pulses that allow the motors to be accelerated or slowed down. The accelerated motion observed during the heat pulses is attributed primarily to the thermal activation of the redox reactions of the H(2)O(2) fuel at the Pt and Au segments and to the decreased viscosity of the aqueous medium at elevated temperatures. The thermally modulated motion during repetitive temperature on/off cycles is highly reversible and fast, with speeds of 14 and 45 microm s(-1) at 25 and 65 degrees C, respectively. A wide range of speeds can be generated by tailoring the temperature to yield a linear speed-temperature dependence. Through the use of nickel-containing nanomotors, the ability to combine the thermally regulated motion of catalytic nanomotors with magnetic guidance is also demonstrated. Such on-demand control of the movement of nanowire motors holds great promise for complex operations of future manmade nanomachines and for creating more sophisticated nanomotors.

Comparison Between Potentiometric and Stripping Voltammetric Detection of Trace Metals: Measurements of Cadmium and Lead in the Presence of Thalium, Indium, and Tin.

Recent advances in ion-selective electrodes have pushed the detection limits of direct potentiometry to the nanomolar concentration range. Here we present a direct comparison of the sensitivity and selectivity of potentiometric and stripping-voltammetric measurements of cadmium and lead. While both techniques offer a similar sensitivity, the potentiometric method offers higher selectivity in the presence of excess of metal ions (e.g., thallium, tin) that commonly interfere in the stripping-voltammetric operation. Because of the complementary nature of the potentiometric and stripping-voltammetric methods, it is recommended that these techniques will be selected based on the specific analytical problem or used in parallel to provide additional analytical information.

Electrochemical sample matrix elimination for trace-level potentiometric detection with polymeric membrane ion-selective electrodes.

Potentiometric sensors are today sufficiently well understood and optimized to reach ultratrace level (subnanomolar) detection limits for numerous ions. In many cases of practical relevance, however, a high electrolyte background hampers the attainable detection limits. A particularly difficult sample matrix for potentiometric detection is seawater, where the high saline concentration forms a major interfering background and reduces the activity of most trace metals by complexation. This paper describes for the first time a hyphenated system for the online electrochemically modulated preconcentration and matrix elimination of trace metals, combined with a downstream potentiometric detection with solid contact polymeric membrane ion-selective microelectrodes. Following the preconcentration at the bismuth-coated electrode, the deposited metals are oxidized and released to a medium favorable to potentiometric detection, in this case calcium nitrate. Matrix interferences arising from the saline sample medium are thus circumvented. This concept is successfully evaluated with cadmium as a model trace element and offers potentiometric detection down to low parts per billion levels in samples containing 0.5 M NaCl background electrolyte.