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.

Open-Form Configurational Isomers of a Tricyanofuran-Type Metastable-State Photoacid.

We determine the presence of four open-form configurational isomers for an unsubstituted metastable-state photoacid (mPAH) of the tricyanofuran (TCF) type in solution, at room temperature, via 2D NMR experiments. Electronic structure calculations are carried out to predict the relative stability of the isomers found experimentally and their isomerization barriers. According to the calculated rate constants for isomerization, the molecule can freely interconvert between the open-form isomers, thereby providing a thermal pathway between the isomers that might be better suited to access the cyclized closed-form configuration and those that are not. In establishing the open form isomeric makeup of the TCF mPAH under study, this work establishes the need to consider the four isomers in further studies on the thermal and excited-state isomerization processes and substituent effect thereon.

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).

Enhanced Fouling Resistance and Antimicrobial Property of Ultrafiltration Membranes Via Polyelectrolyte-Assisted Silver Phosphate Nanoparticle Immobilization.

Ultrafiltration (UF) is a low-pressure membrane that yields higher permeate flux and saves significant operating costs compared to high-pressure membranes; however, studies addressing the combined improvement of anti-organic and biofouling properties of UF membranes are lacking. This study investigated the fouling resistance and antimicrobial property of a UF membrane via silver phosphate nanoparticle (AgPNP) embedded polyelectrolyte (PE) functionalization. Negatively charged polyacrylic acid (PAA) and positively charged polyallylamine hydrochloride (PAH) were deposited on the membrane using a fluidic layer-by-layer assembly technique. AgPNPs were immobilized within the crosslinked "bilayers" (BL) of PAH/PAA. The effectiveness of AgPNP immobilization was confirmed by microprofile measurements on membrane surfaces using a solid contact Ag micro-ion-selective electrode. Upon stable and uniform BL formation on the membrane surface, the permeate flux was governed by a combined effect of PAH/PAA-derived hydrophilicity and surface/pore coverage by the BLs "tightening" of the membrane. When fouled by a model organic foulant (humic acid), the functionalized membrane exhibited a lower flux decline and a greater flux recovery due to the electrostatic repulsion imparted by PAA when compared to the unmodified membrane. The functionalization rendered antimicrobial property, as indicated by fewer attachments of bacteria that initiate the formation of biofilms leading to biofouling.

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.

Visible light-triggered fluorescence and pH modulation using metastable-state photoacids and BODIPY.

Small changes in the pH gradient play a critical role in numerous biological and chemical pathways. Systems capable of monitoring and regulating these changes with high sensitivity and minimum photo-fatigue are in demand. Herein, we propose a visible light-triggered molecular system that allows for reversible regulation of acidity and fluorescence. This robust bi-functional system opens a new horizon towards novel studies that rely on small changes in acid-mediated controlled processes with high sensitivity. The two photosensitive compounds employed, a metastable-state photoacid (mPAH) and a boron-dipyrromethene (BODIPY) derivative, allow for consistent modulation of both fluorescence (based on the working principle of the inner filter effect) and pH (around a magnitude) over multiple cycles.

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.

Visible light-induced ion-selective optodes based on a metastable photoacid for cation detection.

A new platform of ion-selective optodes is presented here to detect cations under thermodynamic equilibrium via ratiometric analysis. This novel platform utilizes a 'one of a kind' visible light-induced metastable photoacid as a reference ion indicator to achieve activatable and controllable sensors. These ion-selective optodes were studied in terms of their stability, sensitivity, selectivity, and theoretical aspects.

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.

Adsorption of Proteins to Thin-Films of PDMS and Its Effect on the Adhesion of Human Endothelial Cells.

This paper describes a simple and inexpensive procedure to produce thin-films of poly(dimethylsiloxane). Such films were characterized by a variety of techniques (ellipsometry, nuclear magnetic resonance, atomic force microscopy, and goniometry) and used to investigate the adsorption kinetics of three model proteins (fibrinogen, collagen type-I, and bovine serum albumin) under different conditions. The information collected from the protein adsorption studies was then used to investigate the adhesion of human dermal microvascular endothelial cells. The results of these studies suggest that these films can be used to model the surface properties of microdevices fabricated with commercial PDMS. Moreover, the paper provides guidelines to efficiently attach cells in BioMEMS devices.

Amplified potentiometric transduction of DNA hybridization using ion-loaded liposomes.

Amplified potentiometric transduction of DNA hybridization based on using liposome 'nanocarriers' loaded with the signaling ions is reported. The liposome-amplified potentiometric bioassay involved the duplex formation, followed by the capture of calcium-loaded liposomes, a surfactant-induced release and highly-sensitive measurements of the calcium signaling ions using a Ca(2+) ion-selective electrode (ISE). The high loading yield of nearly one million signaling ions per liposome leads to sub-fmol DNA detection limits. Factors affecting the ion encapsulation efficiency and signal amplification are evaluated and discussed. The influence of the surfactant lysing agent is also examined. Such use of 'green' calcium signaling ions addresses the inherent toxicity of Ag and CdS nanoparticle tags used in previous potentiometric bioassays. The new strategy was applied for the detection of low levels of E. coli bacteria. It could be readily extended to trace measurements of other important biomolecules in connection to different biorecognition events. The attractive analytical performance makes liposomes a useful addition to the armory of potentiometric bioassays.

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.

Potentiometric detection of DNA hybridization using enzyme-induced metallization and a silver ion selective electrode.

Here, we report on a highly sensitive potentiometric detection of DNA hybridization. The new assay uses a low-volume solid-contact silver ion-selective electrode (Ag(+)-ISE) to monitor the depletion of silver ions induced by the biocatalytic reaction of the alkaline-phosphatase enzyme tag. The resultant potential change of the Ag(+)-ISE, thus, serves as the hybridization signal. Factors affecting the potentiometric hybridization response have been optimized to offer a detection limit of 50 fM (0.2 amol) DNA target. The new potentiometric assay was applied successfully to the monitoring of the 16S rRNA of E. coli pathogenic bacteria to achieve a low detection limit of 10 CFU in the 4 microL sample. Such potentiometric transduction of biocatalytically induced metallization processes holds great promise for monitoring various bioaffinity assays involving common enzyme tags.

Real-time electrochemical monitoring of drug release from therapeutic nanoparticles.

An electrochemical protocol for real-time monitoring of drug release kinetics from therapeutic nanoparticles (NPs) is described. The method is illustrated for repetitive square-wave voltammetric measurements of the reduction of doxorubicin released from liposomes at a glassy-carbon electrode. Such operation couples high sensitivity down to 20 nM doxorubicin with high speed and stability. It can thus monitor in real time the drug release from NP carriers, including continuous measurements in diluted serum. Such direct and continuous monitoring of the drug release kinetics from therapeutic NPs holds great promise for designing new drug delivery NPs with optimal drug release properties. These NPs can potentially be used to deliver many novel compounds such as marine-life derived drugs and hydrophobic drugs with limited water solubility that are usually difficult to be characterized by traditional analytical tools.

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.

REAL-TIME PROBING OF THE GROWTH DYNAMICS OF NANOPARTICLES USING POTENTIOMETRIC ION-SELECTIVE ELECTRODES.

This Communication demonstrates the ability of potentiometric ion-selective electrodes (ISE) to probe the growth dynamics of metal nanoparticles in real-time. The new monitoring capability is illustrated using a solid-contact silver ISE for monitoring the hydroquinone-induced precipitation of silver on gold nanoparticle seeds. Potential-time recordings obtained under different conditions are used to monitor the depletion of the silver ion during the nanoparticle formation and shed useful insights into the growth dynamics of the nanoparticles. Such potentiometric profiles correlate well with the analogous optical measurements. The new real-time electrochemical probing of the particle growth process reflects the direct, rapid and sensitive response of modern ISE to changes in the level of the precipitated metal ion from the bulk solution and holds considerable promise for probing the preparation of different nanoscale materials.

Nanoparticle-induced potentiometric biosensing of NADH at copper ion-selective electrodes.

We demonstrate the first example of using potentiometry at ion-selective electrodes (ISEs) for probing in real-time monitoring of biometallization processes. A copper ISE is used for real-time monitoring of the NADH-mediated reduction of copper in the presence of gold nanoparticle seeds. Such potentiometric detection of NADH is not susceptible to surface fouling common with analogous amperometric measurements of this co-factor. Biosensing of ethanol is illustrated in the presence of alcohol dehydrogenase and NAD(+), along with potentiometric detection of the NADH product at the copper ISE. The concept can be readily expanded to the monitoring of various biometallization processes in connection to different enzymatic transformations and ISE, and used for ultrasensitive detection of bioaffinity interactions in connection to common enzyme tags.