Morpholino-Functionalized Nanochannel Array for Label-Free Single Nucleotide Polymorphisms Detection

Bioinspired Solid-State Nanochannel Sensors: From Ionic Current Signals, Current, and Fluorescence Dual Signals to Faraday Current Signals

Inspired from bioprotein channels of living organisms, constructing "abiotic" analogues, solid-state nanochannels, to achieve "smart" sensing towards various targets, is highly seductive. When encountered with certain stimuli, dynamic switch of terminal modified probes in terms of surface charge, conformation, fluorescence property, electric potential as well as wettability can be monitored via transmembrane ionic current, fluorescence intensity, faraday current signals of nanochannels and so on. Herein, the modification methodologies of nanochannels and targets-detecting application are summarized in ions, small molecules, as well as biomolecules, and systematically reviewed are the nanochannel-based detection means including 1) by transmembrane current signals; 2) by the coordination of current- and fluorescence-dual signals; 3) by faraday current signals from nanochannel-based electrode. The coordination of current and fluorescence dual signals offers great benefits for synchronous temporal and spatial monitoring. Faraday signals enable the nanoelectrode to monitor both redox and non-redox components. Notably, by incorporation with confined effect of tip region of a needle-like nanopipette, glorious in-vivo monitoring is conferred on the nanopipette detector at high temporal-spatial resolution. In addition, some outlooks for future application in reliable practical samples analysis and leading research endeavors in the related fantastic fields are provided.

A label-free ratiometric immunoassay using bioinspired nanochannels and a smart modified electrode

Labeling with redox reporter is often required in developing electrochemical bioassay for most proteins or nucleic acid biomarkers. Herein, a label-free ratiometric immunosensing platform is firstly developed by integrating the antibody-conjugated nanochannels with a smart modified electrode. The electrode modifier is the composite of C₆₀, tetraoctylammonium bromide (TOA⁺) and Prussian blue (PB). Cyclic voltammograms of the ultimate C₆₀-TOA⁺/PB modified electrode exhibited two pairs of peaks at 0.15 V and -0.13 V, ascribing to the redox of PB and C₆₀, respectively. With the addition of K₃[Fe(CN)₆] in the electrolyte solution, the peaks of PB decreased due to the adsorption of [Fe(CN)₆]^3- while the peaks of C₆₀ increased because of the formation of the ternary complex (TC) C₆₀-TOA⁺-[Fe(CN)₆]^3-. As a result, the peak current ratio I_PB/I_TC decreased gradually with the increment of the concentration of [Fe(CN)₆]^3-. For the nanochannels-based immunosensing platform, the steric hindrance of the bioconjugated nanochannels varied with the loading amount of the target CA125, and thus [Fe(CN)₆]^3- passing through the channels was quantitatively affected. And the higher CA125 level was, the less [Fe(CN)₆]^3- concentration was. And thus, the ratio I_PB/I_TC monitored at the C₆₀-TOA⁺/PB modified electrode increased with the increase of the concentration of CA125. The ratiometric immunoassay featured a linear calibration range from 1.0 U mL^-1 to 100 U mL^-1 with a low detection limit of 0.86 U mL^-1. In addition, the ratiometric immunosensing platform demonstrated good specificity and stability as well as acceptable accuracy in overcoming the effect of electrode passivation which was an inherent problem of electroanalysis.

Ultrasensitive plasmon enhanced Raman scattering detection of nucleolin using nanochannels of 3D hybrid plasmonic metamaterial

Detection of cancer biomarker is of great significance in cancer diagnostics. In this work, we propose an ultrasensitive and in situ method for plasmon enhanced Raman scattering (PERS) detection of nucleolin (NCL) using a 3D hybrid plasmonic metamaterial (PM). In this aptasensor, thiolated complementary DNA (cDNA) immobilized on PM can hybridize with Rox-labeled NCL-binding aptamer (AS1411-Rox) to form a rigid double-stranded DNA (dsDNA). When NCL passes through the PM nanochannels under a transmembrane voltage bias, it interacts with AS1411-Rox to form G-quadruplexes (G4-AS1411-Rox), resulting in the release of AS1411-Rox from the nanochannels surface and the decrease in PERS signal of the reporter Rox. This change in PERS signals can be recorded in situ without the interference of external environment. With the help of the enrichment function of nanochannel, the present method is able to achieve fast NCL detection within 10 min with a detection limit as low as 71 pM. Furthermore, our method shows excellent specificity, reversibility, uniformity (relative standard deviation of ~6.86%) and reproducibility (~6.65%), providing a new platform for reliable cancer auxiliary diagnosis and drug screening.

Improvement of Molecular Diagnosis Using Domain-Level Single-Nucleotide Variants by Eliminating Unexpected Secondary Structures

Identification of single-nucleotide variants (SNVs) is of great significance in molecular diagnosis. The problem that should not be ignored in the identification process is that the unexpected secondary structure of the target nucleic acid may greatly affect the detection accuracy. Herein, we proposed a conditional domain-level SNV diagnosis strategy, in which the subsequent SNV detection can only be carried out after eliminating the unexpected secondary structure of target DNA. Specifically, the target DNA is assembled into a rigid double strand, which makes folding the target DNA difficult and the unexpected secondary structure is eliminated. Based on this double-stranded structure, specially designed probes are used to detect double-stranded properties and report abundant domain-level oligonucleotide information to improve the effective information in the detection results and complete domain-level SNV diagnosis. If the unexpected secondary structure is not eliminated, the detector will first detect it and feed back to us, ensuring the accuracy of the subsequent detection results. With the occurrence (or not) of SNV and the change of the SNV site, in the proof-of-concept experiment, we successfully identified the four homologous sequences to be tested related to BRAF gene.

Fabrication, Characterization, and Analytical Application of Silica Nanopore Array-Modified Platinum Electrode

In this work, we report a new approach to fabricate the nanopore array electrode (NAE) by transferring silica nanochannel membrane (SNM) to the surface of Pt electrode (0.5 mm in diameter) sealed by glass capillary (designated as Pt-NAE for simplicity). The SNM is supported via the irreversible covalent-bond formation with the surrounding glass capillary treated by plasma, thus providing long-term stability to Pt-NAE. Meanwhile, this fabrication process does not require pregrafting or premodification of Pt electrode surface, providing well-defined active surface domains. Thanks to the small pore diameter (∼2.3 nm) and negatively charged channel walls, the SNM is permselective and thus the electrochemical behavior of Pt-NAE is dependent on both electrolyte concentration and charge state of redox molecules. The permeability of SNM was determined by the scanning electrochemical microscopy (SECM) approach curve measurements coupled with finite-element simulations from a quantitative viewpoint. The permeability of anionic Ru(CN)₆^4- was varied from 150 to 10.3 μm s^-1 as the electrolyte concentration decreased from 1.0 to 0.01 M, while there is no obvious change for cationic Ru(NH₃)₆³⁺. Finally, the as-prepared Pt-NAE is able to continuously monitor dissolved oxygen for up to 2 h in a solution containing biofouling reagents, exhibiting an enhanced antifouling ability and therefore excellent current stability. We believe the NAE with unique mass transport properties can be extended further for other analytical applications.

In situ growth of nano-gold on anodized aluminum oxide with tandem nanozyme activities towards sensitive electrochemical nanochannel sensing

The growth of nano-gold tandem nanozymes on anodized aluminum oxide is successfully developed using poly-dopamine as an in situ reducing layer for electrochemical nanochannel sensing.

Highly Transparent Cyclic Olefin Copolymer Film with a Nanotextured Surface Prepared by One-Step Photografting for High-Density DNA Immobilization

Compared with conventional glass slides and two-dimensional (2D) planar microarrays, polymer-based support materials and three-dimensional (3D) surface structures have attracted increasing attention in the field of biochips because of their good processability in microfabrication and low cost in mass production, as well as their improved sensitivity and specificity for the detection of biomolecules. In the present study, UV-induced emulsion graft polymerization was carried out on a cyclic olefin copolymer (COC) surface to generate 3D nanotextures composed of loosely stacked nanoparticles with a diameter of approximately 50 nm. The introduction of a hierarchical nanostructure on a COC surface only resulted in a 5% decrease in its transparency at a wavelength of 550 nm but significantly increased the surface area, which markedly improved immobilization density and efficiency of an oligonucleotide probe compared with the functional group and polymer brush-modified substrates. The highest immobilization efficiency of the probes reached 93%, and a limit of detection of 75 pM could be obtained. The hybridization experiment demonstrated that the 3D gene chip exhibited excellent sensitivity for target DNA detection and single-nucleotide polymorphism discrimination. This one-step approach to the construction of nanotextured surfaces on the COC has promising applications in the fields of biochips and immunoassays.

Biomolecule-Functionalized Solid-State Ion Nanochannels/Nanopores: Features and Techniques

Solid-state ion nanochannels/nanopores, the biomimetic products of biological ion channels, are promising materials in real-world applications due to their robust mechanical and controllable chemical properties. Functionalizations of solid-state ion nanochannels/nanopores by biomolecules pave a wide way for the introduction of varied properties from biomolecules to solid-state ion nanochannels/nanopores, making them smart in response to analytes or external stimuli and regulating the transport of ions/molecules. In this review, two features for nanochannels/nanopores functionalized by biomolecules are abstracted, i.e., specificity and signal amplification. Both of the two features are demonstrated from three kinds of nanochannels/nanopores: nucleic acid-functionalized nanochannels/nanopores, protein-functionalized nanochannels/nanopores, and small biomolecule-functionalized nanochannels/nanopores, respectively. Meanwhile, the fundamental mechanisms of these combinations between biomolecules and nanochannels/nanopores are explored, providing reasonable constructs for applications in sensing, transport, and energy conversion. And then, the techniques of functionalizations and the basic principle about biomolecules onto the solid-state ion nanochannels/nanopores are summarized. Finally, some views about the future developments of the biomolecule-functionalized nanochannels/nanopores are proposed.

Biomimetic Nanochannel-Ionchannel Hybrid for Ultrasensitive and Label-Free Detection of MicroRNA in Cells

A biomimetic nanochannel-ionchannel hybrid coupled with electrochemical detector was developed for label-free and ultrasensitive detection of microRNA (miRNA) in cells. Probe single stranded DNA (ssDNA) was first immobilized on the outer surface of the nanochannel-ionchannel hybrid membrane, which can hybridize with the target miRNA in cells. Due to the unique mass transfer property of the hybrid, the DNA-miRNA hybridization kinetics can be sensitively monitored in real-time using the electrochemical technique. More importantly, due to the super small size of the ionchannels, the DNA probe immobilization and hybridization process can be carried out on the outer surface of the ionchannel side, which can effectively avoid the blockage and damage of channels and thus considerably enhance the reproducibility and accuracy of the method. Using this strategy, the miRNA ranging from 0.1 fM to 0.1 μM can be facilely detected with a low detection limit of 15.4 aM, which is much lower than most reported work. The present strategy provides a sensitive and label-free miRNA detection platform, which will be of great significance in biomedical research and clinical diagnosis.

A unique FRET approach toward detection of single-base mismatch DNA in BRCA1 gene

Early detection of mutation carriers in predisposing genes such as BRCA1 plays an important role in disease prevention. This work developed a quantum dots-based (QDs-based) fluorescence resonance energy transfer (FRET) technique for the detection of single-base mismatch DNA in BRCA1 gene. The FRET between QDs as the donor and silver nanocluster (AgNCs) as the acceptor was designed by the strong interaction between CdTe QDs with appropriate size and dsDNA through binding to its major groove. The dsDNA was formed by the hybridization of ssDNA labeled to AgNCs with target DNA, which introduced CdTe QDs into the major grooves to place the AgNCs in close proximity to the QDs. The complementary and single-base mismatch DNA led to obviously different FRET signals. The FRET signal linearly correlated to the concentration of single-base mismatch DNA in the range of 1.5 × 10^-10-1.0 × 10^-6 mol L^-1. The proposed method showed a detection limit of 80 pmol L^-1 and the sensitivity comparable to the previously reported assays, indicating promising potential for single nucleotide polymorphisms diagnosis in clinical application.

Nanochannel-Ion Channel Hybrid Device for Ultrasensitive Monitoring of Biomolecular Recognition Events

We propose an in situ and label-free method for detection of biomolecular recognition events by use of a nanochannel-ion channel hybrid device integrated with an electrochemical detector. The aptamer is first immobilized on the outer surface of the nanochannel-ion channel hybrid. Its binding with target thrombin in solution considerably regulates the mass-transfer behavior of the device owing to the varied surface charge density and effective channel size. Via the electrochemical detector, the changed mass-transport property can be monitored in real time, which enables in situ and label-free detection of thrombin-aptamer recognition. The solution pH has a significant influence on detection sensitivity. Under optimal pH conditions, a detection limit as low as 0.22 fM thrombin can be achieved, which is much lower than most reported work. The present nanofluidic device provides a simple, ultrasensitive, and label-free platform for monitoring biomolecular recognition events, which would hold great potential in exploring the functions and reaction mechanisms of biomolecules in living systems.

Integrated Solid-State Nanopore Electrochemistry Array for Sensitive, Specific, and Label-Free Biodetection

Nanopore ionic current measurement is currently a prevailing readout and offers considerable opportunities for bioassays. Extending conventional electrochemistry to nanoscale space, albeit noteworthy, remains challenging. Here, we report a versatile electrochemistry array established on a nanofluidic platform by controllably depositing gold layers on the two outer sides of anodic aluminum oxide (AAO) nanopores, leading to form an electrochemical microdevice capable of performing amperometry in a label-free manner. Electroactive species ferricyanide ions passing through gold-decorated nanopores act as electrochemical indicator to generate electrolytic current signal. The electroactive species flux that dominates current signal response is closely related to the nanopore permeability. Such well-characteristic electrolytic current-species flux correlation lays a premise for quantitative electrochemical analysis. As a proof-of-concept demonstration, we preliminarily verify the analytical utility by detection of nucleic acid and protein at picomolar concentration levels. Universal surface modification and molecule assembly, specific target recognition and reliable signal output in nanopore enable direct electrochemical detection of biomolecules without the need of cumbersome probe labeling and signal amplification.

Advances in Nanoporous Anodic Alumina-Based Biosensors to Detect Biomarkers of Clinical Significance: A Review

There is a strong and growing demand for compact, portable, rapid, and low-cost devices to detect biomarkers of interest in clinical and point-of-care diagnostics. Such devices aid in early diagnosis of diseases without the need to rely on expensive and time-consuming large instruments in dedicated laboratories. Over the last decade, numerous biosensors have been developed for detection of a wide range of clinical biomarkers including proteins, nucleic acids, growth factors, and bacterial enzymes. Various transduction techniques have been reported based on biosensor technology that deliver substantial advances in analytical performance, including sensitivity, reproducibility, selectivity, and speed for monitoring a wide range of human health conditions. Nanoporous anodic alumina (NAA) has been used extensively for biosensing applications due to its inherent optical and electrochemical properties, ease of fabrication, large surface area, tunable properties, and high stability in aqueous environment. This review focuses on NAA-based biosensing systems for detection of clinically significant biomarkers using various detection techniques with the main focus being on electrochemical and optical transduction methods. The review covers an overview of the importance of biosensors for biomarkers detection, general (surface and structural) properties and fabrication of NAA, and NAA-based biomarker sensing systems.

Diagnostic Applications of Morpholinos and Label-Free Electrochemical Detection of Nucleic Acids

Diagnostic applications of morpholinos take advantage of their unique properties including backbone charge neutrality, a weak impact of ionic strength on their hybridization behavior, and their resistance to enzymatic degradation. This chapter overviews how these properties have advanced transduction and other capabilities useful for the analysis of nucleic acids. In many cases, the benefits stem from electrostatic mechanisms; for example, use of low ionic strengths improves sensitivity of detection while decreasing background signals because only the nucleic acid analyte is charged. While most literature reports focus on in vitro assays in buffer, morpholinos have been also used for biodistribution measurements of species such as fungal rRNA and miRNA. After reviewing the diagnostic applications of morpholinos, the chapter describes preparation of morpholino monolayers on metal supports for electrochemical diagnostics and the procedure for performing label-free detection of DNA from changes in surface capacitance.

DNA nanoflower blooms in nanochannels: a new strategy for miRNA detection

DNA nanoflower blooming was employed in the nanochannels of porous anodic alumina to build a nanochannel platform for miRNA detection with excellent sensitivity, selectivity and reproducibility.

Asymmetric Nanochannel-Ionchannel Hybrid for Ultrasensitive and Label-Free Detection of Copper Ions in Blood

Nanochannel/nanopre based analysis methods have attracted increasing interest in recent years due to their exquisite ability to reveal changes in molecular volume. In this work, a highly asymmetric nanochannel-ionchannel hybrid coupled with an electrochemical technique was developed for copper ion (Cu²⁺) detection. Polyglutamic acid (PGA) was modified in a nanochannel array of porous anodic alumina (PAA). When different concentrations of Cu²⁺ were introduced into the nanochannel-ionchannel hybrid in a neutral environment, a Cu²⁺-PGA chelation reaction occurs, resulting in varied current-potential (I-V) properties of the nanochannel-ionchannel hybrid. When PAA was immersed in a low pH solution, the Cu²⁺-PGA complex dissociated. On the basis of the change in ionic current, a label-free assay for Cu²⁺ was achieved along with the ability to regenerate and reuse the constructed platform. Because of the unique mass transfer property of the nanochannel-ionchannel hybrid combined with the highly amplified ionic current magnitude of the nanochannel array, significantly increased assay sensitivity was achieved, as expected. To evaluate the applicability of the present methodology for detecting Cu²⁺ in a real sample, the Cu²⁺ content in real blood samples was analyzed. The results demonstrate that the present method shows excellent selectivity with high sensitivity toward Cu²⁺ detection in real blood samples.

Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection

In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN _x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.

Ultrasensitive Capture, Detection, and Release of Circulating Tumor Cells Using a Nanochannel-Ion Channel Hybrid Coupled with Electrochemical Detection Technique

With the growing demands of the early, accurate, and sensitive diagnosis for cancers, the development of new diagnostic technologies becomes increasingly important. In this study, we proposed a strategy for efficient capture and sensitive detection of circulating tumor cells (CTCs) using an array nanochannel-ion channel hybrid coupled with an electrochemical detection technique. The aptamer probe was immobilized on the ion channel surface to couple with the protein overexpressed on the CTCs membrane. Through this special molecular recognition, CTCs can be selectively captured. The trapped CTCs cover the ion channel entrance efficiently, which will dramatically block the ionic flow through channels, resulting in a varied mass-transfer property of the nanochannel-ion channel hybrid. On the basis of the changed mass-transfer properties, the captured CTCs can be sensitively detected using the electrochemical linear sweep voltammetry technique. Furthermore, due to the amplified response of array channels compared to that of a single channel, the detection sensitivity can be enhanced greatly. The results showed that acute leukemia CCRF-CEM (a type of CTC) concentration as low as 100 cells mL^-1 can be successfully captured and detected. The present method provides a simple, sensitive, and label-free technique for CTCs capture, detection, and release, which would hold great potential in the early clinical diagnosis and treatment of cancers.

Electrostatic Cycling of Hybridization Using Nonionic DNA Mimics

This study demonstrates efficient electrostatic control of surface hybridization through use of morpholinos, a charge-neutral DNA mimic, as the immobilized "probes". In addition to being compatible with low ionic strengths, use of uncharged probes renders the field interaction specific to the nucleic acid analyte. In contrast to DNA probes, morpholino probes enable facile cycling between hybridized and dehybridized states within minutes. Impact of ionic strength and temperature on the effectiveness of electrostatics to direct progress of hybridization is evaluated. Optimal electrostatic control is found when stability of probe-analyte duplexes is set so that electrostatics can efficiently switch between the forward (hybridization) and reverse (dehybridization) directions.

Ultrasensitive Detection of MicroRNAs with Morpholino-Functionalized Nanochannel Biosensor

Here, we demonstrate a phosphorodiamidate morpholino oligos (PMO)-functionalized nanochannel biosensor for label-free detection of microRNAs (miRNAs) with ultrasensitivity and high sequence specificity. PMO, as a capture probe, was covalently anchored on the nanochannel surface. Because of the neutral character and high sequence-specific affinity of PMO, hybridization efficiency between PMO and miRNAs was enhanced, thus largely decreasing background signals and highly improving the detection specificity and sensitivity. The miRNAs detection was realized through observing the change of surface charge density when PMO/miRNAs hybridization occurred. Not only could the developed biosensor specifically discriminate complementary miRNAs (Let-7b) from noncomplementary miRNAs (miR-21) and one-base mismatched miRNAs (Let-7c), but also it could detect target miRNAs in serum samples. In addition, this nanochannel-based biosensor attained a reliable limit of detection down to 1 fM in PBS and 10 fM in serum sample, respectively. It is expected that such a new method will benefit miRNA detection in clinical diagnosis.

Functional "Janus" Annulus in Confined Channels

Scattered Au 3D nanoparticles form distinct functional regions with an uncovered internal surface in confined channels, named the "Janus" annulus. Electrochemical impedance spectroscopy responses to the variations in DNA self-assembly and hybridization in the channels decorated by the "Janus" annulus are presented. Single nucleotide mutations are further detected in a linear DNA chain, including terminal base polymorphisms.

Ionic Transport through Chemically Functionalized Hydrogen Peroxide-Sensitive Asymmetric Nanopores

We describe the fabrication of a chemical-sensitive nanofluidic device based on asymmetric nanopores whose transport characteristics can be modulated upon exposure to hydrogen peroxide (H2O2). We show experimentally and theoretically that the current-voltage curves provide a suitable method to monitor the H2O2-mediated change in pore surface characteristics from the electronic readouts. We demonstrate also that the single pore characteristics can be scaled to the case of a multipore membrane whose electric outputs can be readily controlled. Because H2O2 is an agent significant for medical diagnostics, the results should be useful for sensing nanofluidic devices.