Single Conducting Polymer Nanowire Based Sequence-Specific, Base-Pair-Length Dependant Label-free DNA Sensor

Smartphone-powered, ultrasensitive, and selective, portable and stable multi-analyte chemiresistive immunosensing platform with PPY/COOH-MWCNT as bioelectrical transducer: Towards point-of-care TBI diagnosis

Traumatic Brain Injury, one of the significant causes of mortality and morbidity, affects worldwide and continues to be a diagnostic challenge. The most desirable and partially met clinical need is to simultaneously detect the disease-specific-biomarkers in a broad range of readily available body fluids on a single platform with a rapid, low-cost, ultrasensitive and selective device. Towards this, an array of interdigitated microelectrodes was fabricated on commercially existing low-cost single-side copper cladded printed-circuit-board substrate followed by the bioelectrodes preparation through covalent immobilization of brain injury specific biomarkers on carboxylic functionalized multi-walled carbon nanotubes embedded polypyrrole nanocomposite modified interdigitated microelectrodes. Subsequently, the immunological binding events were transduced as the normalized change in bioelectrode resistance with and without the target analyte via current-voltage analysis. As proof of concept, current-voltage responses were primarily recorded using a conventional probe station, and later, a portable handheld-electronic-readout was developed for the point-of-care application. The data compilation and analysis were carried out using the in-house developed android-based mobile app. Notably, the smartphone powered the readout through a PL-2303 serial connector, avoiding integrating power sources with the readout. Further, this technology can be adapted to other point-of-care biosensing applications.

Label-free, ultrasensitive and rapid detection of FDA-approved TBI specific UCHL1 biomarker in plasma using MWCNT-PPY nanocomposite as bio-electrical transducer: A step closer to point-of-care diagnosis of TBI

Traumatic Brain Injury (TBI), a major cause of mortality and neurological disability affecting people of all ages worldwide, remains a diagnostic and therapeutic challenge to date. Rapid, ultra-sensitive, selective, and wide-range detection of TBI biomarkers in easily accessible body fluids is an unmet clinical need. Considering this, in this work, we report the design and development of a facile, label-free, highly stable and sensitive, chemi-impedance-based sensing platform for rapid and wide range detection of Ubiquitin-carboxy terminal hydrolase L1 (UCHL1: FDA-approved TBI specific plasma biomarker), using carboxylic functionalized MWCNTs embedded polypyrrole (PPY) nanocomposites (PPY/f-MWCNT). The said nanocomposites were synthesized using chemical oxidative polymerization method. Herein, the functionalized MWCNTs are used as conducting fillers so as to increase the polymer's dielectric constant according to the micro-capacitor model, thereby augmenting both DC electrical conductivity and AC dielectric property of the nanocomposite. The proposed immunosensing platform comprises of PPY/f-MWCNT modified interdigitated microelectrode (IDμEs) array, on which anti-UCHL1-antibodies are immobilized using suitable covalent chemistry. The AC electrical characterization of the nanocomposite modified IDμEs, with and without the antibodies, was performed through generic capacitance vs. frequency (C-F, 1 KHz - 1 MHz) and capacitance vs. applied bias (C-V, 0.1 V-1 V) measurements, using an Agilent B1500A parametric analyzer. The binding event of UCHL1 peptides to anti-UCHL1-antibodies was transduced in terms of normalised changes in parallel capacitance, via the C-F analysis. Further, we have tested the detection efficiency of the said immunoassay against UCHL1 spiked human plasma samples in the concentration range 10 fg/mL - 1 μg/mL. The proposed sensing platform detected UCHL1 in spiked-plasma samples linearly in the range of 10 fg/mL - 1 ng/mL with a sensitivity and LoD of 4.22 ((ΔC/C₀)/ng.mL^-1)/cm² and 0.363 fg/mL, respectively. Further, it showed excellent stability (30 weeks), repeatability, reproducibility, selectivity and interference-resistance. The proposed approach is label-free, and if desired, can be used in conjunction with DC measurements, for biosensing applications.

Artificial Intelligence-Based Portable Bioelectronics Platform for SARS-CoV-2 Diagnosis with Multi-nucleotide Probe Assay for Clinical Decisions

In the context of the recent pandemic, the necessity of inexpensive and easily accessible rapid-test kits is well understood and need not be stressed further. In light of this, we report a multi-nucleotide probe-based diagnosis of SARS-CoV-2 using a bioelectronics platform, comprising low-cost chemiresistive biochips, a portable electronic readout, and an Android application for data acquisition with machine-learning-based decision making. The platform performs the desired diagnosis from standard nasopharyngeal and/or oral swabs (both on extracted and non-extracted RNA samples) without amplifying the viral load. Being a reverse transcription polymerase chain reaction-free hybridization assay, the proposed approach offers inexpensive, fast (time-to-result: ≤ 30 min), and early diagnosis, as opposed to most of the existing SARS-CoV-2 diagnosis protocols recommended by the WHO. For the extracted RNA samples, the assay accounts for 87 and 95.2% test accuracies, using a heuristic approach and a machine-learning-based classification method, respectively. In case of the non-extracted RNA samples, 95.6% decision accuracy is achieved using the heuristic approach, with the machine-learning-based best-fit model producing 100% accuracy. Furthermore, the availability of the handheld readout and the Android application-based simple user interface facilitates easy accessibility and portable applications. Besides, by eliminating viral RNA extraction from samples as a pre-requisite for specific detection, the proposed approach presents itself as an ideal candidate for point-of-care SARS-CoV-2 diagnosis.

Towards point-of-care diagnosis of Alzheimer's disease: Multi-analyte based portable chemiresistive platform for simultaneous detection of β-amyloid (1-40) and (1-42) in plasma

Label-free simultaneous detection of Alzheimer's disease (AD) specific biomarkers Aβ40 and Aβ42 peptides on a single platform using polypyrrole nanoparticle-based chemiresistive biosensors is reported here. The proposed interdigitated-microelectrode based inexpensive multisensor-platform can concurrently detect Aβ40 and Aβ42 in spiked-plasma in the range of 10-14 - 10-6 g/mL (with LoDs being 5.71 and 9.09 fg/mL, respectively), enabling the estimation of diagnostically significant Aβ42/Aβ40 ratio. A detailed study has been undertaken here to record the individual sensor responses against spiked-plasma samples with varying amounts and proportions of the two target peptides, towards enabling disease-progression monitoring using the Aβ-ratio. As compared to the existing cost-ineffective brain-imaging techniques such as PET and MRI, and the high-risk CSF based invasive AD biomarkers detecting procedures, the proposed approach offers a viable alternative for affordable point-of-care AD diagnostics, with possible usage in performance evaluation of therapeutic drugs. Towards point-of-care applications, the portable readout used in this work was conjugated with an android-based mobile app for data-acquisition and analysis.

Amplification-free, sequence-specific 16S rRNA detection at 1 aM

A nucleic acid amplification-free, optics-free platform has been demonstrated for sequence-specific detection of Escherichia coli (E. coli) 16S rRNA at 1 aM (10-18 M) against a 106-fold (1 pM) background of Pseudomonas putida (P. putida) RNA. This work was driven by the need for simple, rapid, and low cost means for species-specific bacterial detection at low concentration. Our simple, conductometric sensing device functioned by detecting blockage of a nanopore fabricated in a sub-micron-thick glass membrane. Upon sequence-specific binding of target 16S rRNA, otherwise charge-neutral, PNA oligonucleotide probe-polystyrene bead conjugates become electrophoretically mobile and are driven to the glass nanopore of lesser diameter, which is blocked, thereby generating a large, sustained and readily observable step decrease in ionic current. No false positive signals were observed with P. putida RNA when this device was configured to detect E. coli 16S rRNA. Also, when a universal PNA probe complementary to the 16S rRNA of both E. coli and P. putida was conjugated to beads, a positive response to rRNA of both bacterial species was observed. Finally, the device readily detected E. coli at 10 CFU mL-1 in a 1 mL sample, also against a million-fold background of viable P. putida. These results suggest that this new device may serve as the basis for small, portable, low power, and low-cost systems for rapid detection of specific bacterial species in clinical samples, food, and water.

Recent advances in nanowires-based field-effect transistors for biological sensor applications

Nanowires (NWs)-based field-effect transistors (FETs) have attracted considerable interest to develop innovative biosensors using NWs of different materials (i.e. semiconductors, polymers, etc.). NWs-based FETs provide significant advantages over the other bulk or non-NWs nanomaterials-based FETs. As the building blocks for FET-based biosensors, one-dimensional NWs offer excellent surface-to-volume ratio and are more suitable and sensitive for sensing applications. During the past decade, FET-based biosensors are smartly designed and used due to their great specificity, sensitivity, and high selectivity. Additionally, they have the advantage of low weight, low cost of mass production, small size and compatible with commercial planar processes for large-scale circuitry. In this respect, we summarize the recent advances of NWs-based FET biosensors for different biomolecule detection i.e. glucose, cholesterol, uric acid, urea, hormone, proteins, nucleotide, biomarkers, etc. A comparative sensing performance, present challenges, and future prospects of NWs-based FET biosensors are discussed in detail.

PNA versus DNA in electrochemical gene sensing based on conducting polymers: study of charge and surface blocking effects on the sensor signal

In this communication, we present an in-depth study of DNA/DNA, DNA/PNA and PNA/PNA hybridisation on a conducting polymer-modified electrode, measured by means of electrochemical impedance spectroscopy (EIS). DNA or PNA nucleic base sequence probes (where DNA stands for deoxyribonucleic acid and PNA for peptide nucleic acid) were covalently attached onto the sensor surface. As PNA is a non-charged variant of DNA, we investigate the effects of the surface charge and surface blocking by the surface confined probe/target nucleic bases complexes onto the kinetics of redox reaction of Fe(CN)₆^3-/4- couple occurring at the electrode/solution interface that provides electrochemical readout for hybridisation. A range of hybridisation detection experiments were performed, where the surface charge and surface charge density were varied, through varying the charged nature of the probe and the target (i.e. PNA or DNA) and the density of surface-bound PNA and DNA probes. To further the understanding of these effects on the measured electrochemical signal, kinetic studies of the hybridisation reactions were undertaken, and the equilibrium binding constants and binding rate constants for the hybridisation reactions were obtained. The study provides valuable insights to guide future designs of biosensors.

PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli) 16S rRNA at 10 fM, which corresponds to ~100-1000 colony forming units/mL (CFU/mL) depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD) of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.

An accurate cost effective DFT approach to study the sensing behaviour of polypyrrole towards nitrate ions in gas and aqueous phases

A variety of low cost computational methods are evaluated to accurately calculate the interaction energy between polypyrrole and nitrate ions.

A microfluidic electrochemical biosensor based on multiwall carbon nanotube/ferrocene for genomic DNA detection of Mycobacterium tuberculosis in clinical isolates

Herein we present a microfluidic-multiplexed platform that integrates electrochemical sensors based on carbon nanotubes associated with ferrocene as redox marker (carbon nanotube (CNT)/ferrocene) for direct detection of pathogenic viral DNA from Hepatitis C and genomic DNA from Mycobacterium tuberculosis in clinical isolates. By operating the fluidic device under high flow (150 μl/min), the formation of a very thin depletion layer at the sensor surface (δS = 230 nm) enhances the capture rate up to one DNA strand per second. By comparison, this capture rate is only 0.02 molecule/s in a static regime without flow. This fluidic protocol allows thus enhancing the limit of detection of the electrochemical biosensor from picomolar in bulk solution to femtomolar with a large dynamic range from 0.1 fM to 1 pM. Kinetics analysis also demonstrates an enhancement of the rate constant of electron transfer (kS) of the electrochemical process from 1 s(-1) up to 6 s(-1) thanks to the geometry of the miniaturized fluidic electrochemical cell. This microfluidic device working under high flow allows selective direct detection of a Mycobacterium tuberculosis (H37Rv) rpoB allele from clinical isolate extracted DNA. We envision that a microfluidic approach under high flow associated with a multiwall CNT/ferrocene sensor could find useful applications as the point-of-care for multi-target diagnostics of biomarkers in real samples.

Exploitation of Nanotechnology for the Monitoring of Waterborne Pathogens: State-of-the-Art and Future Research Priorities

Contaminated drinking water is one of the most important environmental contributors to the human disease burden. Monitoring of water for the presence of pathogens is an essential part of ensuring drinking water safety. In order to assess water quality it is essential to have methods available to sample and detect the type, level and viability of pathogens in water which are effective, cheap, quick, sensitive, and where possible high throughput. Nanotechnology has the potential to drastically improve the monitoring of waterborne pathogens when compared to conventional approaches. To date, there have been no reviews that outline the applications of nanotechnology in this area despite increasing exploitation of nanotechnology for this purpose. This review is therefore the first overview of the state-of-the-art in the application of nanotechnology to waterborne pathogen sampling and detection schemes. Research in this field has been centered on the use of engineered nanomaterials. The effectiveness and limitations of nanomaterial-based approaches is outlined. A future outlook of the advances that are likely to emerge in this area, as well as recommendations for areas of further research are provided.

Electrochemical DNA hybridization sensors based on conducting polymers

Conducting polymers (CPs) are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective.

Sequence-specific DNA detection at 10 fM by electromechanical signal transduction

Target DNA fragments at 10 fM concentration (approximately 6 × 10(5) molecules) were detected against a DNA background simulating the noncomplementary genomic DNA present in real samples using a simple, PCR-free, optics-free approach based on electromechanical signal transduction. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is highly desired for a range of diverse applications. We previously described a potentially low-cost device for sequence-specific nucleic acid detection based on conductance change measurement of a pore blocked by electrophoretically mobilized bead-(peptide nucleic acid probe) conjugates upon hybridization with target nucleic acid. Here, we demonstrate the operation of our device with longer DNA targets, and we describe the resulting improvement in the limit of detection (LOD). We investigated the detection of DNA oligomers of 110, 235, 419, and 1613 nucleotides at 1 pM to 1 fM and found that the LOD decreased as DNA length increased, with 419 and 1613 nucleotide oligomers detectable down to 10 fM. In addition, no false positive responses were obtained with noncomplementary, control DNA fragments of similar length. The 1613-base DNA oligomer is similar in size to 16S rRNA, which suggests that our device may be useful for detection of pathogenic bacteria at clinically relevant concentrations based on recognition of species-specific 16S rRNA sequences.

Intrinsically conducting polymer nanowires for biosensing

The fabrication of conductive polymer nanowires and their sensing of nucleic acids, proteins and pathogens is reviewed in this feature article.

Biosensors in the small scale: methods and technology trends

This study presents a review on biosensors with an emphasis on recent developments in the field. A brief history accompanied by a detailed description of the biosensor concepts is followed by rising trends observed in contemporary micro- and nanoscale biosensors. Performance metrics to quantify and compare different detection mechanisms are presented. A comprehensive analysis on various types and subtypes of biosensors are given. The fields of interest within the scope of this review are label-free electrical, mechanical and optical biosensors as well as other emerging and popular technologies. Especially, the latter half of the last decade is reviewed for the types, methods and results of the most prominently researched detection mechanisms. Tables are provided for comparison of various competing technologies in the literature. The conclusion part summarises the noteworthy advantages and disadvantages of all biosensors reviewed in this study. Furthermore, future directions that the micro- and nanoscale biosensing technologies are expected to take are provided along with the immediate outlook.

DNA hybridization assay at individual, biofunctionalized zinc oxide nanowires

Reliable and efficient identification of DNA is a major goal in on-site diagnostics. One dimensional nanostructures like nanowires (NW) represent potential sensor structures due to their extreme surface-to-bulk ratio, enabling enhanced biomolecule binding which results in optimal signals. While silicon NW are already well studied, NW made from other materials with promising properties like ZnO are not yet established as NW sensor material for bioanalytics. Here we demonstrate the DNA functionalization of ZnO NW even at the single NW level and their successful application in a DNA hybridization assay.

Anisotropic growth control of polyaniline nanostructures and their morphology-dependent electrochemical characteristics

Polyaniline (PANI) is one of the most widely investigated conducting polymers and is considered to be of practical use for many future applications. Here, we first demonstrate that the anisotropic growth of PANI at the nanometer scale can be kinetically controlled by employing a polymeric stabilizer, poly(N-vinylpyrrolidone). The polymerization rate became slower in the presence of the stabilizer (the rate constants calculated at the initial stage decreased with increasing concentration of the stabilizer), yielding PANI nanostructures with lower aspect ratios. Therefore, it is believed that the stabilizer sterically restricts the directional fiber growth mechanism governing PANI chain growth in aqueous solution. Three PANI nanostructures, specifically nanospheres, nanorods, and nanofibers, were fabricated and their oxidation/protonation levels were investigated systematically. It was found that the nanofibers had the most outstanding oxidation/protonation level accompanied by structural ordering (note that the only difference between the polymerization conditions in each case was the concentration of the stabilizer). We also examine the electrochemical properties of PANI nanostructure electrodes in three-electrode and two-electrode (actual capacitor cell) configurations. The intrinsic charge-transport ability of individual nanostructures strongly affected the electrochemical properties of the electrodes. Briefly, the nanofiber electrode had faster electrode kinetics and better capacitance than the nanorods and nanospheres. Lastly, an extrinsic factor, the interparticle contact resistance, also turned out to noticeably influence the capacitances of the electrodes.

Toward single-DNA electrochemical biosensing by graphene nanowalls

Graphene oxide nanowalls with extremely sharp edges and preferred vertical orientation were deposited on a graphite electrode by using electrophoretic deposition in an Mg(2+)-GO electrolyte. Using differential pulse voltammetry (DPV), reduced graphene nanowalls (RGNWs) were applied for the first time, in developing an ultra-high-resolution electrochemical biosensor for detection of the four bases of DNA (G, A, T, and C) by monitoring the oxidation signals of the individual nucleotide bases. The extremely enhanced electrochemical reactivity of the four free bases of DNA, single-stranded DNA, and double-stranded DNA (dsDNA) at the surface of the RGNW electrode was compared to electrochemical performances of reduced graphene nanosheet (RGNS), graphite, and glassy carbon electrodes. By increasing the number of DPVs up to 100 scans, the RGNW electrode exhibited an excellent stability with only 15% variation in the oxidation signals, while for the RGNS electrode no detectable signals relating to T and C of 0.1 μM dsDNA were observed. The linear dynamic detection range of the RGNW electrode for dsDNA was checked in the wide range of 0.1 fM to 10 mM, while for the RGNS electrode, it was from 2.0 pM to <10 mM. The lower limits of dsDNA detection of the RGNW and RGNS electrodes were estimated as 9.4 zM (∼5 dsDNA/mL) and 5.4 fM, respectively. The RGNWs were efficient in label-free detection of single nucleotide polymorphisms of 20 zM oligonucleotides (∼10 DNA/mL) having a specific sequence. Therefore, the RGNWs can effectively contribute to the development of ultra-high-sensitive electrochemical biosensors with single-DNA resolutions.

Virus-polymer hybrid nanowires tailored to detect prostate-specific membrane antigen

We demonstrate the de novo fabrication of a biosensor, based upon virus-containing poly(3,4-ethylene-dioxythiophene) (PEDOT) nanowires, that detects prostate-specific membrane antigen (PSMA). This development process occurs in three phases: (1) isolation of a M13 virus with a displayed polypeptide receptor, from a library of ≈10(11) phage-displayed peptides, which binds PSMA with high affinity and selectivity, (2) microfabrication of PEDOT nanowires that entrain these virus particles using the lithographically patterned nanowire electrodeposition (LPNE) method, and (3) electrical detection of the PSMA in high ionic strength (150 mM salt) media, including synthetic urine, using an array of virus-PEDOT nanowires with the electrical resistance of these nanowires for transduction. The electrical resistance of an array of these nanowires increases linearly with the PSMA concentration from 20 to 120 nM in high ionic strength phosphate-buffered fluoride (PBF) buffer, yielding a limit of detection (LOD) for PSMA of 56 nM.