DNA‐Based Nanopore Sensing

Nanopore sensing is an attractive, label‐free approach that can measure single molecules. Although initially proposed for rapid and low‐cost DNA sequencing, nanopore sensors have been successfully employed in the detection of a wide variety of substrates. Early successes were mostly achieved based on two main strategies by 1) creating sensing elements inside the nanopore through protein mutation and chemical modification or 2) using molecular adapters to enhance analyte recognition. Over the past five years, DNA molecules started to be used as probes for sensing rather than substrates for sequencing. In this Minireview, we highlight the recent research efforts of nanopore sensing based on DNA‐mediated characteristic current events. As nanopore sensing is becoming increasingly important in biochemical and biophysical studies, DNA‐based sensing may find wider applications in investigating DNA‐involving biological processes.     

Analyte‐Triggered DNA‐Probe Release from a Triplex Molecular Beacon for Nanopore Sensing

A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex‐forming molecular beacon and a stem‐forming DNA component that is modified with a host–guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α‐hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point‐of‐care diagnostics with a portable nanopore kit in the future.     

Reversing current rectification to improve DNA‐sensing sensitivity in conical nanopores

Herein, we report the ultrasensitive DNA detection through designing an elegant nanopore biosensor as the first case to realize the reversal of current rectification direction for sensing. Attributed to the unique asymmetric structure, the glass conical nanopore exhibits the sensitive response to the surface charge, which can be facilely monitored by ion current rectification curves. In our design, an enzymatic cleavage reaction was employed to alter the surface charge of the nanopore for DNA sensing. The measured ion current rectification was strongly responsive to DNA concentrations, even reaching to the reversed status from the negative ratio (?6.5) to the positive ratio (+16.1). The detectable concentration for DNA was as low as 0.1 fM. This is an ultrasensitive and label‐free DNA sensing approach, based on the rectification direction‐reversed amplification in a single glass conical nanopore.     

DNA‐Assisted Self‐Assembly of Pyrene Foldamers

Folding in the tides : Upon hybridization, pyrene molecules assemble through interstrand stacking interactions to form double‐stranded, helical structures. Structural organization of the pyrene molecules is an intrinsic property of the oligoaryl part and takes place independently of the sequence of the attached DNA. Pyrene helicity is most pronounced in a bi‐segmental chimera, in which a DNA stem is present only at one end of the pyrene section.

     

A Universal Strategy for Aptamer‐Based Nanopore Sensing through Host–Guest Interactions inside α‐Hemolysin

Nanopore emerged as a powerful single‐molecule technique over the past two decades, and has shown applications in the stochastic sensing and biophysical studies of individual molecules. Here, we report a versatile strategy for nanopore sensing by employing the combination of aptamers and host–guest interactions. An aptamer is first hybridized with a DNA probe which is modified with a ferrocene?cucurbit[7]uril complex. The presence of analytes causes the aptamer–probe duplex to unwind and release the DNA probe which can quantitatively produce signature current events when translocated through an α‐hemolysin nanopore. The integrated use of magnetic beads can further lower the detection limit by approximately two to three orders of magnitude. Because aptamers have shown robust binding affinities with a wide variety of target molecules, our proposed strategy should be universally applicable for sensing different types of analytes with nanopore sensors.     

Electro‐nano Diagnostic Platforms for Simultaneous Detection of Multiple Cancer Biomarkers

In this study, a bimetallic nanomaterial‐based electrochemical immunosensor was developed for the detection of carcinoembryonic antigen (CEA) and vascular endothelial growth factor (VEGF) cancer biomarkers at the same time. CEA and VEGF biomarkers are indicators for colon and breast cancers and stomach cancers, respectively. During the study, gold nanoparticle (AuNp), lead nanoparticle (PbNp), copper nanoparticle (CuNp) and magnetic gamma iron(III)oxide (γFe₂O₃ Np) were synthesized, characterized and used together for the first time in the structure of an electrochemical biosensor based on anti‐CEA and anti‐VEGF. For this purpose, Au SPE based sandwich immunosensor was fabricated by using labeled anti‐CEA (labeled with Pb⁺²) and labeled anti‐VEGF (labeled with Cu⁺²). As a result, CEA and VEGF biomarkers were detected following the oxidation peaks of label metals (Pb⁺² and Cu⁺²) by using differential pulse voltammetry. After the experimental parameters were optimized, the linear range was found in the concentration range between 25 ng/mL and 600 ng/mL with the relative standard deviation (RSD) value of (n=3 for 600 ng/mL) 3.33 % and limit of detection (LOD) value of 4.31 ng/mL for CEA biomarker. On the other hand, the linear range was found in the concentration range between 0.2 ng/mL and 12.5 ng/mL with the RSD value of (n=3 for 12.5 ng/mL) 5.31 % and LOD value of 0.014 ng/mL for VEGF biomarker. Lastly, sample application studies for synthetic plasma sample and interference studies with dopamine, ascorbic acid, BSA, cysteine and IgG were carried out.     

Detection of structured single‐strand DNA via solid‐state nanopore

Nanopore is a single‐molecule analysis method which also employed electrophoresis has achieved promising single‐molecule detections. In this study, we designed two kinds of confined spaces by fabricating solid‐state nanopores with desirable diameters to study the structured single‐strand DNA of C‐rich quadruplex. For the nanopore whose diameter is larger than the quadruplex size, the DNA molecule could directly translocate through the nanopore with extremely high speed. For the nanopore whose diameter is smaller than the quadruplex size, DNA molecule which is captured by nanopore could return to the solution without translocation or unzip the quadruplex structure into single‐strand and then pass the nanopore. This study certifies that choosing a suitable sensing interface is the vital importance of observing detailed single‐molecule information. The solid‐state nanopores hold the great potential to study the structural dynamics of quadruplex DNA molecule.     

Sensing Enzymatic Activity by Exposure and Selection of DNA‐Encoded Probes

A sensing approach is applied to encode quantitative enzymatic activity information into DNA sequence populations. The method utilizes DNA‐linked peptide substrates as activity probes. Signal detection involves chemical manipulation of a probe population downstream of sample exposure and application of purifying, selective pressure for enzyme products. Selection‐induced changes in DNA abundance indicate sample activity. The detection of protein kinase, protease, and farnesyltransferase activities is demonstrated. The assays were employed to measure enzyme inhibition by small molecules and activity in cell lysates using parallel DNA sequencing or quantitative PCR. This strategy will allow the extensive infrastructure for genetic analysis to be applied to proteomic assays, which has a number of advantages in throughput, sensitivity, and sample multiplexing.     

Comparison of Different Strategies on DNA Chip Fabrication and DNA‐Sensing: Optical and Electrochemical Approaches

New strategies for the construction of DNA chips and the detection of DNA hybridization will be discussed in this review. The focus will be on the use of polypyrrole as a linker between a substrate and oligonucleotide probes. The modification step is based on the electrochemical copolymerization of pyrrole and oligonucleotides bearing a pyrrole group on its 5′ end. This strategy was employed for the immobilization of oligonucleotides on millimeter‐sized electrodes, microelectrode arrays, as well as for the local structuring of homogeneous gold surfaces. Our approaches for the localized patterning of gold surfaces will be also discussed. Localized immobilization was achieved by using an electrospotting technique, where a micropipette served as an electrochemical cell where spot sizes with 800 μm diameters were fabricated. The use of a microcell using a Teflon covered metal needle with a cavity of 100 μm resulted in immobilized probe spots of 300 μm. Scanning electrochemical microscopy (SECM) was also used, and surface modifications of 100 μm were obtained depending on the experimental conditions. Different detection methods were employed for the reading of the hybridization event: fluorescence imaging, surface plasmon resonance imaging (SPRI), photocurrent measurements, and voltamperometric measurements using intercalators. Their advantages concerning the various immobilization strategies will also be discussed.     

Mitochondrial‐DNA‐Targeted IrIII‐Containing Metallohelices with Tunable Photodynamic Therapy Efficacy in Cancer Cells

The development of DNA‐targeted photodynamic therapy (PDT) agents for cancer treatment has drawn substantial attention. Herein, the design and synthesis of dinuclear Ir^III‐containing luminescent metallohelices with tunable PDT efficacy that target mitochondrial DNA in cancer cells are reported. The metallohelices are fabricated using dynamic imine‐coupling chemistry between aldehyde end‐capped fac‐Ir(ppy)₃ handles and linear alkanediamine spacers, followed by reduction of the imine linkages. The length and odd–even character of the diamine alkyl linker determined the stereochemistry (helicates vs. mesocates). Compared to the helicates, the mesocates exhibit improved apoptosis‐induction upon white‐light irradiation. Molecular docking studies indicate that the mesocate with a proper length of diamine spacers shows stronger affinity for the minor groove of DNA. This study highlights the potential of DNA‐targeting Ir^III‐containing metallohelices as PDT agents.     

Microwave‐Assisted Modular Fabrication of Nanoscale Luminescent Metal‐Organic Framework for Molecular Sensing

Miniaturizing the size of metal‐organic framework (MOF) crystals to the nanometer scale is challenging, but it provides more advanced applications without changing the characteristic features itself. It is especially useful to investigate the correlation between the porous properties and the interfacial structures of nanocrystals. Using amino acids as capping agents, nanoscale Tb‐MOF‐76 is fabricated rapidly by means of microwave‐assisted methods. Both the modular effects of the amimo acids and the acid–base environment of the reaction medium have an important impact on the morphologies and dimensions of Tb‐MOF‐76. The structures of the samples are confirmed by powder X‐ray diffraction, and the morphologies are characterized by SEM. Photoluminescence studies reveal that these Tb‐MOF‐76 materials exhibit a green emission corresponding to the transition ⁵D₄→⁷F_J of Tb³⁺ ions under UV‐light excitation, which is sensitive to small organic molecules in solution.     

Ultrasensitive Simultaneous Detection of Multiple Rare Modified Nucleosides as Promising Biomarkers in Low-Put Breast Cancer DNA Samples for Clinical Multi-Dimensional Diagnosis

Early cancer diagnosis is essential for successful treatment and prognosis, and modified nucleosides have attracted widespread attention as a promising group of cancer biomarkers. However, analyzing these modified nucleosides with an extremely low abundance is a great challenge, especially analyzing multiple modified nucleosides with a different abundance simultaneously. In this work, an ultrasensitive quantification method based on chemical labeling, coupled with LC-MS/MS analysis, was established for the simultaneous quantification of 5hmdC, 5fdC, 5hmdU and 5fdU. Additionally, the contents of 5mdC and canonical nucleosides could be obtained at the same time. Upon derivatization, the detection sensitivities of 5hmdC, 5fdC, 5hmdU and 5fdU were dramatically enhanced by several hundred times. The established method was further applied to the simultaneous detection of nine nucleosides with different abundances in about 2 μg genomic DNA of breast tissues from 20 breast cancer patients. The DNA consumption was less than other overall reported quantification methods, thereby providing an opportunity to monitor rare, modified nucleosides in precious samples and biology processes that could not be investigated before. The contents of 5hmdC, 5hmdU and 5fdU in tumor tissues and normal tissues adjacent to the tumor were significantly changed, indicating that these three modified nucleosides may play certain roles in the formation and development of tumors and be potential cancer biomarkers. While the detection rates of 5hmdC, 5hmdU and 5fdU alone as a biomarker for breast cancer samples were 95%, 75% and 85%, respectively, by detecting these three cancer biomarkers simultaneously, two of the three were 100% consistent with the overall trend. Therefore, simultaneous detection of multiple cancer biomarkers in clinical samples greatly improved the accuracy of cancer diagnosis, indicating that our method has great application potential in clinical multidimensional diagnosis.