Bubble-Mediated Ultrasensitive Multiplex Detection of Metal Ions in Three-Dimensional DNA Nanostructure-Encoded Microchannels

Peptides in the detection of metal ions

By means of their specific interactions with different metal ions, naturally occurring proteins control structures and functions of many biological processes and functions in organisms. In view of natural metallopeptides, scientists have proposed artificial peptides which coordinate with metal ions through their functional groups either for introducing a special reactivity or for constructing various sensors. However, the design of new peptide ligands requires a deep understanding of the structures, assembly properties, and dynamic behaviors of such peptides. This review briefly describes detection strategies of metal ions via coordination to the binding sites in peptides. The principles and functions of sensing systems are described as well. We also highlight some examples of a metal-induced peptide self-assembly with relevance to biotechnology applications.

Super-resolution Multispectral Imaging Nanoimmunosensor for Simultaneous Detection of Diverse Early Cancer Biomarkers

In medical diagnosis, relying on only one type of biomarker is insufficient to accurately identify cancer. Blood-based multicancer early detection can help identify more than one type of cancer from a single blood sample. In this study, a super-resolution multispectral imaging nanoimmunosensor (srMINI) based on three quantum dots (QDs) of different color conjugated with streptavidin was developed for the simultaneous screening of various cancer biomarkers in blood at the single-molecule level. In the experiment, the srMINI chip was used to simultaneously detect three key cancer biomarkers: carcinoembryonic antigen (CEA), C-reactive protein (CRP), and alpha-fetoprotein (AFP). The srMINI chip exhibited 108 times higher detection sensitivity of 0.18-0.5 ag/mL (1.1-2.6 zM) for these cancer biomarkers than commercial enzyme-linked immunosorbent assay kits because of the absence of interfering signals from the substrate, establishing considerable potential for multiplex detection of cancer biomarkers in blood. Therefore, the simultaneous detection of various cancer biomarkers using the developed srMINI chip with high diagnostic precision and accuracy is expected to play a decisive role in early diagnosis or community screening as a single-molecule biosensor.

Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity

A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.

A capillary-based microfluidic chip with the merits of low cost and easy fabrication for the rapid detection of acute myocardial infarction

Point-of-care testing methods currently utilize rapid, portable, inexpensive, and multiplexed on-site detection. Microfluidic chips have become a very promising platform with broad development prospects due to their breakthrough improvement in miniaturization and integration. However, the conventional microfluidic chips still have disadvantages, such as difficulty in fabrication processing, long production time and high cost, which hinder its applications in the fields of POCT and in vitro diagnostics. In this study, a capillary-based microfluidic chip with the characteristics of low cost and easy fabrication was developed for the rapid detection of acute myocardial infarction (AMI). Several short capillaries, which were already conjugated with the capture antibodies respectively, were connected by peristaltic pump tubes and then formed the working capillary. Two working capillaries were encapsulated in the plastic shell and ready for the immunoassay. Multiplex detection of Myoglobin (Myo), cardiac troponin I (cTnI) and creatine kinase-MB (CK-MB) were chosen to demonstrate the feasibility and analytical performance of the microfluidic chip, which requires rapid and accurate detection during diagnosis and therapy for AMI. The capillary-based microfluidic chip required tens of minutes to prepared, and its cost was less than $1. The limit of detection (LOD) was 0.5 ng/mL for Myo, 0.1 ng/mL for cTnI and 0.5 ng/mL for CK-MB respectively. The capillary-based microfluidic chips with easy fabrication and low cost hold promise for the portable and low-cost detection of target biomarkers.

A cell-surface-anchored DNA probe coupled with hybridization chain reaction enzyme-free dual signal amplification for sensitive electrochemical detection of the cellular microenvironment

The cellular microenvironment plays key roles in regulating physiological processes. However, it is still a challenge to detect it with quantification. Here, a simple, biocompatible, and universal strategy based on cell surface-anchored specific DNAzymes and hybridization chain reaction enzyme-free signal amplification for cellular microenvironment electrochemical detection is presented. In this strategy, the cell could be captured on the surface of the electrode via aptamer-target recognition. On the other hand, the DNAzyme hybridized with the substrate strand as a metal ion probe was anchored on the surface of the cell. In the presence of metal ions, the substrate strand could be cleaved into two fragments by the DNAzyme and released from the cell surface. Then, the DNA modified gold nanoparticles (AuNPs) could be captured on the electrode. Subsequently, an alternative hybridization reaction of two hairpin probes was triggered by the carried initiators forming nicked double helices. For signal readout, hemin could be inserted into the double-helix DNA long chain via electrostatic interaction, which could electro-reduce hydrogen peroxide to generate an electrochemical signal. Based on the intrinsic advantages of DNAzymes, including rapid kinetics, high sensitivity, and high selectivity, and the signal amplification strategy, this method should be able to monitor and semi-quantify target metal ions in the cellular microenvironment. Furthermore, this method shows potential for various targets by employing different DNA probes in the cellular microenvironment, providing a platform for bioanalysis.

Recent Developments in DNA-Nanotechnology-Powered Biosensors for Zika/Dengue Virus Molecular Diagnostics

Zika virus (ZIKV) and dengue virus (DENV) are highly contagious and lethal mosquito-borne viruses. Global warming is steadily increasing the probability of ZIKV and DENV infection, and accurate diagnosis is required to control viral infections worldwide. Recently, research on biosensors for the accurate diagnosis of ZIKV and DENV has been actively conducted. Moreover, biosensor research using DNA nanotechnology is also increasing, and has many advantages compared to the existing diagnostic methods, such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). As a bioreceptor, DNA can easily introduce a functional group at the 5' or 3' end, and can also be used as a folded structure, such as a DNA aptamer and DNAzyme. Instead of using ZIKV and DENV antibodies, a bioreceptor that specifically binds to viral proteins or nucleic acids has been fabricated and introduced using DNA nanotechnology. Technologies for detecting ZIKV and DENV can be broadly divided into electrochemical, electrical, and optical. In this review, advances in DNA-nanotechnology-based ZIKV and DENV detection biosensors are discussed.

DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects

DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.

Digital Microfluidic Thermal Control Chip-Based Multichannel Immunosensor for Noninvasively Detecting Acute Myocardial Infarction

Rapid and automated detection of acute myocardial infarction (AMI) at its developing stage is very important due to its high mortality rate. To quantitatively diagnose AMI, Myo, CK-MB, and cTnI are chosen as three biomarkers, which are usually detected through an immunosorbent assay, such as the enzyme-linked immunosorbent assay. However, the approach poses many drawbacks, such as long detection time, the cumbersome process, the need for professionals, and the difficulty of realizing automatic operation. Here, a multichannel digital microfluidic (DMF) thermal control chip integrated with a sandwich-based immunoassay strategy is proposed for the automated, rapid, and sensitive detection of AMI biomarkers. A miniaturized temperature control module is integrated on the back of the DMF chip, meeting the temperature requirement for the immunoassay. With this DMF thermal control chip, sample and reagent consumption are reduced to several microliters, significantly alleviating reagent consumption and sample dependence, and the automated and multichannel detection of biomarkers can be achieved. In this work, the simultaneously noninvasive detection of the human serum sample containing the three biomarkers of AMI is also achieved within 30 min, which improves the diagnostic accuracy of AMI. Due to the features of automation and miniaturization, the multichannel immunosensor can be used in community hospitals to increase the speed of diagnosis of patients with various acute diseases.

DNA Nanotechnology-Based Biosensors and Therapeutics

Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.

Hybridization chain reaction and its applications in biosensing

To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.

Controllable design of a nano-bio aptasensing interface based on tetrahedral framework nucleic acids in an integrated microfluidic platform

The limited reaction time and sample volume in the confined space of microfluidic devices give considerable importance to the development of more effective biosensing interfaces. Herein, the self-assembling of tetrahedral framework nucleic acids (FNAs) with controllable size on the interface of the microfluidic microchannels is studied. Compared with macroscopic turbulence control on traditional micro-structured microfluidic surface, the novel FNA-engineered microfluidic interface successfully constructs a 3D reaction space at nanoscale by raising DNA probes away from the surface. This FNA interface dramatically improves the reaction kinetics during molecular recognition due to extremely ordered orientation, configuration and density of DNA probes on the surface. Finally, the FNA-engineered interface is applied in a novel multi-functional microfluidic platform, towards a "one-stop" assay of Escherichia coli O157: H7 (E. coli O157: H7), integrating capture, release, enrichment, cell culture and antimicrobial susceptibility testing (AST). With the FNA-aptamer probe, we achieved an enhanced bacterial detecting efficiency (10 CFU/mL) plus excellent selectivity and precision. The appicability was strongly demonstrated when the biosensor was successfully applied in real samples, including the analysis of antibiotic susceptibility and minimum inhibitory concentration (MIC) of E. coli O157: H7 among different antibiotics. The application of FNA interface will open a wide avenue for the development of microfluidic biosensors for other pathogenic microorganisms or circulating tumor cells (CTC) simply by changing the aptamers.

Multifunctional magnetic iron oxide nanoparticles: an advanced platform for cancer theranostics

Multifunctional magnetic nanoparticles and derivative nanocomposites have aroused great concern for multimode imaging and cancer synergistic therapies in recent years. Among the rest, functional magnetic iron oxide nanoparticles (Fe3O4 NPs) have shown great potential as an advanced platform because of their inherent magnetic resonance imaging (MRI), biocatalytic activity (nanozyme), magnetic hyperthermia treatment (MHT), photo-responsive therapy and drug delivery for chemotherapy and gene therapy. Magnetic Fe3O4 NPs can be synthesized through several methods and easily surface modified with biocompatible materials or active targeting moieties. The MRI capacity could be appropriately modulated to induce response between T1 and T2 modes by controlling the size distribution of Fe3O4 NPs. Besides, small-size nanoparticles are also desired due to the enhanced permeation and retention (EPR) effect, thus the imaging and therapeutic efficiency of Fe3O4 NP-based platforms can be further improved. Here, we firstly retrospect the typical synthesis and surface modification methods of magnetic Fe3O4 NPs. Then, the latest biomedical application including responsive MRI, multimodal imaging, nanozyme, MHT, photo-responsive therapy and drug delivery, the mechanism of corresponding treatments and cooperation therapeutics of multifunctional Fe3O4 NPs are also be explained. Finally, we also outline a brief discussion and perspective on the possibility of further clinical translations of these multifunctional nanomaterials. This review would provide a comprehensive reference for readers to understand the multifunctional Fe3O4 NPs in cancer diagnosis and treatment.

Dual-Wavelength Electrochemiluminescence Ratiometric Biosensor for NF-κB p50 Detection with Dimethylthiodiaminoterephthalate Fluorophore and Self-Assembled DNA Tetrahedron Nanostructures Probe

In this work, we fabricated a dual-wavelength electrochemiluminescence ratiometric biosensor based on electrochemiluminescent resonance energy transfer (ECL-RET). In this biosensor, Au nanoparticle-loaded graphitic phase carbon nitride (Au-g-C₃N₄) as a donor and Au-modified dimethylthiodiaminoterephthalate (TAT) analogue (Au@TAT) as an acceptor were investigated for the first time. Besides, tetrahedron DNA probe was immobilized onto Au-g-C₃N₄ to improve the binding efficiency of the transcription factor and ECL ratiometric changes on the basis of the ratio of ECL intensities at 595 and 460 nm, which were obtained through the formation of a sandwich structure of DNA probe-antigen-antibody. Our biosensor achieved the assay of NF-κB p50 with a detection limit of 5.8 pM as well as high stability and specificity.

Simultaneous Detection of Multiple Tumor Markers in Blood by Functional Liquid Crystal Sensors Assisted with Target-Induced Dissociation of Aptamer

Multiplex detection of tumor markers in blood with high specificity and high sensitivity is critical to cancer diagnosis, treatment, and prognosis. Herein, we demonstrate a strategy for simultaneous detection of multiple tumor markers in blood by functional liquid crystal (LC) sensors assisted with target-induced dissociation (TID) of an aptamer for the first time. Magnetic beads (MBs) coated with an aptamer (apt1) are employed to specifically capture target proteins in blood. After incubation of the obtained protein-coated MBs with duplexes of another aptamer (apt2) and signal DNA, sandwich complexes of apt1/protein/apt2 are formed on the MBs due to specific recognition of target proteins by apt2, which induces release of signal DNA into the aqueous solution. Subsequently, signal DNA is specifically recognized by highly sensitive DNA-laden LC sensors. Using this strategy, a 3D printed optical cell was employed to enable simultaneous detection of multiple tumor markers such as carcinoembryonic antigen (CEA), alpha-fetoprotein (AFP), and prostate specific antigen (PSA) with high specificity and high sensitivity. Overall, this effective and low-cost multiplex approach takes advantage of the easy separation of MBs, high specificity of aptamer-based recognition, and high sensitivity of functional LC sensors. Plus, it offers a performance that is competitive to that of commercial ELISA kits without potential interference from hemolysis, which makes it very promising in multiplex detection of tumor markers in clinical applications.

Near-IR emissive rare-earth nanoparticles for guided surgery

Intraoperative image-guided surgery (IGS) has attracted extensive research interests in determination of tumor margins from surrounding normal tissues. Introduction of near infrared (NIR) fluorophores into IGS could significantly improve the in vivo imaging quality thus benefit IGS. Among the reported NIR fluorophores, rare-earth nanoparticles exhibit unparalleled advantages in disease theranostics by taking advantages such as large Stokes shift, sharp emission spectra, and high chemical/photochemical stability. The recent advances in elements doping and morphologies controlling endow the rare-earth nanoparticles with intriguing optical properties, including emission span to NIR-II region and long life-time photoluminescence. Particularly, NIR emissive rare earth nanoparticles hold advantages in reduction of light scattering, photon absorption and autofluorescence, largely improve the performance of nanoparticles in biological and pre-clinical applications. In this review, we systematically compared the benefits of RE nanoparticles with other NIR probes, and summarized the recent advances of NIR emissive RE nanoparticles in bioimaging, photodynamic therapy, drug delivery and NIR fluorescent IGS. The future challenges and promises of NIR emissive RE nanoparticles for IGS were also discussed.

A glass nanopore ionic sensor for surface charge analysis

Surface charge-based nanopore characterization techniques unfold unique properties and provide a powerful platform for a variety of sensing applications. In this paper, we have proposed a nanoconfined inner wall surface charge characterization method with glass nanopores. The glass nanopores were functionalized with DNA aptamers that were designed for mercury (Hg²⁺) ion immobilization by forming thymine–Hg²⁺–thymine structures. The surface charge of the nanopores was modulated by surface chemistry and Hg²⁺ ion concentrations and analysed by combining zeta potential measurements on glass slides and the ionic current rectification ratio of the nanopores. Also, 1 pM Hg²⁺ ions could be detected by the nanopores.

Surface charge-based nanopore characterization techniques unfold unique properties and provide a powerful platform for a variety of sensing applications.

A versatile biomolecular detection platform based on photo-induced enhanced Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) as one of the effective tools for sensitive and selective detection of biomolecules has attracted tremendous attention. Here, we construct a versatile biomolecular detection platform based on photo-induced enhanced Raman spectroscopy (PIERS) effect for ultrasensitive detection of multiple analytes. In our PIERS sensor, we exploit the molecular recognition capacity of aptamers and the high affinity of aptamers with analyte to trigger TiO₂@AgNP substrates binding with Raman tag-labeled gold nanoparticles probes via analyte, thus forming sandwich complexes. Additionally, combining plasmonic nanoparticles with photo-activated substrates allows PIERS sensor to achieve increased sensitivity beyond the normal SERS effect upon ultraviolet irradiation. Accordingly, the PIERS can be implemented for analysis of multiple analytes by designing different analyte aptamers, and we further demonstrate that the constructed PIERS sensor can serve as a versatile detection platform for sensitively analyzing various biomolecules including small molecules (adenosine triphosphate (ATP), limit of detection (LOD) of 0.1 nM), a biomarker (thrombin, LOD of 50 pM), and a drug (cocaine, LOD of 5 nM). Therefore, this versatile biomolecular detection platform based on PIERS effect for ultrasensitive detection of multiple analytes holds great promise to be a practical tool.

Wavelength distinguishable signal quenching and enhancing toward photoactive material 3,4,9,10-perylenetetracarboxylic dianhydride for simultaneous assay of dual metal ions

Photoelectrochemical (PEC) assay with low background, simple instrumentation and high sensitivity has deemed as one of the most potential strategies to simultaneous multi-component detection. How to distinguish photocurrent changes caused by various targets on a single sensing platform thus becomes the key issue to be resolved. Herein, we innovatively proposed a multiplex PEC biosensor based on wavelength distinguishable signal quenching and enhancing toward photoactive material 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) for simultaneous assay of dual metal ions. Briefly, S1 and S2 ssDNA containing sensitizer methylene blue and quencher ferrocene (termed as MB-S1 and Fc-S2), respectively, were first generated through target Pb²⁺ and Mg²⁺-induced DNAzyme-assisted target recycling, which thereafter were modified on PTCDA sensing platform specifically via host-guest recognition with β-cyclodextrin (β-CD). Interestingly, the sensitizer MB could enhance photocurrent of PTCDA under the excitation wavelength of 623 nm and 590 nm, respectively, while the quencher Fc just quencher the photocurrent of PTCDA under the excitation wavelength of 590 nm, thereby achieving wavelength distinguishable signal quenching and enhancing toward photoactive material PTCDA for simultaneous assay of dual metal ions. As a result, the conceived biosensor for Mg²⁺ and Pb²⁺ detection realized high sensitivity with detection limit of 0.3 pM and 0.3 nM, respectively. The proposed strategy not only for the first time achieved the discrimination of varied PEC signal caused by two targets with usage of sole photoelectric material, but also realized the simultaneous multiplex assay on a single sensing platform, providing a new way for constructing effective and sensitive PEC biosensor for multi-component detection.

Hierarchically spacing DNA probes on bio-based nanocrystal for spatial detection requirements

Sterically spacing and locating functional matters at the nanoscale exert critical effects on their application, especially for the fluorescence probes whose aggregation causes emission quenching. Here we achieved a hierarchical spacing strategy of DNA fluorescence probes for ion detection via locating them separately on rod-like cellulose nanocrystals (CNCs) and further isolating CNCs by pre-grafting long molecular chains. Controlling chemical structure of CNC and location degree could adjust the inter-space of DNA probes (with a molecular length of ca. 3.6 nm) in a range of 3.5-6.5 nm with a gradient about 0.2 nm. A length up to micrometer scale of the CNC nanorods was necessary to provide DNA probes with well-separated grafting locations and enough freedom, which brought a vast linear detection range from 10 nmol/L to 5 μmol/L of Hg²⁺ concentration. The abundant reactive sites on CNC allowed a grafting pre-location of poly (tert-butyl acrylate) (PtBA) to promote the isolation of DNA probes. Controlled radical polymerization was employed to adjust the length of PtBA molecular chains, which increased the linear sensitivity coefficient of Hg²⁺ detection by ca. 2.5 times. This hierarchical nanoscale spacing concept based on chemical design can hopefully conduce to the development of biosensor and medical diagnosis. A hierarchical spacing strategy was applied to separate DNA fluorescent probes on CNCs and detect ion concentration linearly. The first-level spacing was to locate probes uniformly on CNCs, obtaining a wide linear range; and the second-level spacing was to isolate CNCs with polymer, obtaining an increased linear coefficient.

Rapid and Ultrasensitive Quantification of Multiplex Respiratory Tract Infection Pathogen via Lateral Flow Microarray based on SERS Nanotags

Respiratory tract infections (RTIs) are severe acute infectious diseases, which require the timely and accurate identification of the pathogens involved so that the individual treatment plan can be selected, including optimized use of antibiotics. However, high throughput and ultrasensitive quantification of multiple nucleic acids is a challenge in a point of care testing (POCT) device.

Methods: Herein, we developed a 2×3 microarray on a lateral flow strip with surface enhanced Raman scattering (SERS) nanotags encoding the nucleic acids of 11 common RTI pathogens. On account of the signal magnification of encoded SERS nanotags in addition to the high surface area to volume ratio of the nitrocellulose (NC) membrane, rapid quantification of the 11 pathogens with a broad linear dynamic range (LDR) and ultra-high sensitivity was achieved on one lateral flow microarray.

Results: The limit of detection (LOD) for influenza A, parainfluenza 1, parainfluenza 3, respiratory syncytial virus, coxiella burnetii, legionella pneumophila, influenza B, parainfluenza 2, adenovirus, chlamydophila pneumoniae, and mycoplasma pneumoniae were calculated to be 0.031 pM, 0.030 pM, 0.038 pM, 0.038 pM, 0.040 pM, 0.039 pM, 0.035 pM, 0.032 pM, 0.040 pM, 0.039 pM, and 0.041 pM, respectively. The LDR of measurement of the target nucleic acids of the eleven RTI pathogens were 1 pM-50 nM, which span 5 orders of magnitude.

Conclusions: We anticipate this novel approach could be widely adopted in the early and precise diagnosis of RTI and other diseases.

Superwettable colloidal crystal micropatterns on butterfly wing surface for ultrasensitive detection

HYPOTHESIS

Ultrasensitive detections with enrichment approaches based on hydrophilic-hydrophobic patterns have attracted increasing attention in the early diagnosis and treatment of diseases. However, most of these techniques involve complicated micro-fabrications and chemical modifications to achieve their specific pattern substrate wettability. Hence, the development of a simple and effective approach for the construction of new surface wettability techniques for ultrasensitive detection is with great expectations.

EXPERIMENTS

We present a simple approach to fabricate the superwettable colloidal crystal (CC) micropatterns on superhydrophobic Morpho butterfly wing surface for the ultrasensitive detection. The superwettable CC micropatterns were easily obtained by infiltrating and self-assembling monodispersed silica colloidal nanoparticles on the plasma treated butterfly wing patterns. The analytes could be enriched onto the hydrophilic CC area due to the wettability difference between the hydrophilic CC area and the superhydrophobic substrate.

FINDINGS

It was demonstrated that the detection limit of thrombin was down to 1.8 × 10^-13 mol L^-1 based on the fluorophore-labeled aptamer. Moreover, with two-dimensional position codes of these CC micropatterns for different probes, the multiplex detection capability was also demonstrated with great accuracy. As the elimination of complex instruments and chemical modifications, this proposed platform offers a simple strategy for ultrasensitive multiplex detection in practical applications.

Label-Free and Enzyme-Free Colorimetric Detection of Pb2+ Based on RNA Cleavage and Annealing-Accelerated Hybridization Chain Reaction

A label-free and enzyme-free colorimetric sensor for rapid detection of Pb²⁺ is reported, which is based on the strategy of DNAzyme-mediated RNA cleavage combined with an annealing-accelerated DNA hybridization chain reaction (HCR). As a trigger DNA, the substrate strand (S_TM) of DNAzyme can initiate HCR effectively. However, when it is cleaved by DNAzyme in the presence of Pb²⁺, the separation of DNA functional domains leads to a serious decrease in HCR efficiency. As a result, the difference in Pb²⁺ concentration converts into the difference of DNA assembly, which eventually leads to the color change of colloidal gold nanoparticles (AuNPs). In this work, a DNA strand (cGR5) completely complementary to the catalytic strand (GR5) of DNAzyme is used to improve the dissociation of S_TM to enhance the HCR efficiency. In addition, the simple operation of DNA annealing is first used to accelerate the HCR process, enabling the Pb²⁺ detection to be completed in about 30 min. As advantages of high sensitivity, good selectivity, strong anti-interference ability, and good practical performance are achieved, it is anticipated that the cheap and simple colorimetric sensor will be helpful for on-site detection of environmental and food samples.

A "time-frozen" technique in microchannel used for the thermodynamic studies of DNA origami

The emergence of DNA origami greatly accelerated the development of DNA nanotechnology. A thorough understanding of origami thermodynamics is very important for both fundamental studies and practical applications. These thermodynamic transitions usually take place in several seconds or even less, and are very difficult to monitor by conventional methods. Numerous tests are required to characterize the origami molecule's behaviors at different temperatures, which is very labor-intensive and time-consuming. In this paper, an axially distributed temperature gradient along a capillary was formed in a spatially varying temperature field. In such a temperature gradient, the origami molecule's thermodynamic processes occur and remain stable at every position along the capillary's microchannel. It looks like the time of the thermodynamic process is frozen along the microchannel. With this method, the origami molecule's thermodynamic characteristics at different temperatures can be obtained in a single experiment, and rapid processes can be monitored with ease by conventional methods for an adequate time period at low cost. In order to show its potential abilities, this method has been demonstrated in applications which the origami's assembly, denaturation and strand displacement are carry out in a flowing or stationary solution.

Programmable and Multifunctional DNA-Based Materials for Biomedical Applications

DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg²⁺ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.

Simultaneous detection and determination of mercury (II) and lead (II) ions through the achievement of novel functional nucleic acid-based biosensors

The serious threats of mercury (Hg²⁺) and lead (Pb²⁺) ions for the public health makes it important to achieve the detection methods of the ions with high affinity and specificity. Metal ions usually coexist in some environment and foodstuff or clinical samples. Therefore, it is very necessary to develop a fast and simple method for simultaneous monitoring the amount of metal ions, especially when Hg²⁺ and Pb²⁺ coexist. DNAzyme-based biosensors and aptasensors have been highly regarded for this purpose as two main groups of the functional nucleic acid (FNA)-based biosensors. In this review, we summarize the recent achievements of functional nucleic acid-based biosensors for the simultaneous detection of Hg²⁺ and Pb²⁺ ions in two main optical and electrochemical groups. The tremendous interest in utilizing the various nanomaterials is also highlighted in the fabrication of the FNA-based biosensors. Finally, some results are presented based on the advantages and disadvantages of the studied FNA-based biosensors to compare their validation.

Framework-Nucleic-Acid-Enabled Biosensor Development

Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.

MoS2 Nanoprobe for MicroRNA Quantification Based on Duplex-Specific Nuclease Signal Amplification

MicroRNAs (miRNAs) play significant regulatory roles in physiologic and pathologic processes and are considered as important biomarkers for disease diagnostics and therapeutics. Simple, fast, sensitive, and selective detection of miRNAs, however, is challenged by their short length, low abundance, susceptibility to degradation, and homogenous sequence. Here, we report a novel design of nanoprobes for highly sensitive and selective detection of miRNAs based on MoS₂-loaded molecular beacons (MBs) and duplex-specific nuclease (DSN)-mediated signal amplification (DSNMSA). We show that MoS₂ nanosheets not only exhibit high affinity toward MBs but also act as an efficient quencher for absorbed MBs. The strong fluorescence-quenching ability of MoS₂ in combination with cyclic DSNMSA contributes to the superior sensitivity of our method, with a limit of detection 4 orders of magnitude lower than that of traditional hybridization methods. Moreover, the nanoprobes also show high selectivity for discriminating homogenous miRNA sequences with one-base differences because of the discrimination ability of MBs and DSN. Furthermore, we demonstrate that the MoS₂-loaded MB nanoprobes can be utilized for multiplexed detection of miRNAs. Given its high sensitivity and specificity, as well as the multiplexed function; this novel method as an effective tool shows a great promise for simultaneous quantitative analysis of multiple miRNAs in biomedical research and clinical diagnosis.

Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing

Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.

Logic Catalytic Interconversion of G-Molecular Hydrogel

By incorporating hemin into G-quadruplex (G₄) during cation-templated self-assembly between guanosine and KB(OH)₄, we have constructed an artificial enzyme hydrogel (AEH)-based system for the highly sensitive and selective detection of Pb²⁺. The sensing strategy is based on a Pb²⁺-induced decrease in AEH activity. Because of the higher efficiency of Pb²⁺ for stabilizing G₄ compared with K⁺, the Pb²⁺ ions substitute K⁺ and trigger hemin release from G₄, thus giving rise to a conformational interconversion accompanied by the loss of enzyme activity. The Pb²⁺-induced catalytic interconversion endows the AEH-based system with high sensitivity and selectivity for detecting Pb²⁺. As a result, the AEH-based system shows an excellent response for Pb²⁺ in the range from 1 pM to 50 nM with a limit of detection of ∼0.32 pM, which is much lower than that of the previously reported G₄-DNAzyme. We also demonstrate that this AEH-based system exhibits high selectivity toward Pb²⁺ over other metal ions. Furthermore, two two-input INHIBIT logic gates have been constructed via switching of the catalytic interconversion induced by K⁺ and Pb²⁺ or K⁺ and pH. Given its versatility, this AEH-based system provides a novel platform for sensing and biomolecular computation.

Ultrasensitive Detection of Metal Ions with DNA Nanostructure

In spite of its greatly scientific and technological importance, developing rapid, low cost and sensitive microarray sensors for onsite monitoring heavy metal contamination remains challenging. Here we develop a DNA nanostructured microarray (DNM) with a tubular three-dimensional sensing surface and an ordered nanotopography for rapid and sensitive multiplex detection of heavy metal ions. In our design, DNA tetrahedral-structured probes (TSPs) are used to engineer the sensing interface with spatially resolved and density-tunable sensing spots, improving the micro-confined molecular recognition. Meanwhile, a bubble-mediated shuttle reaction inside the DNM-functionalized microchannel improves the target-capturing efficiency. Thus, the sensitive and selective detection of multiple heavy metal ions (i.e., Hg²⁺, Ag⁺, and Pb²⁺) with this novel DNM biosensor can be achieved within 5 min. Moreover, the detection limit is down to 10, 10, and 20 nM for Hg²⁺, Ag⁺, and Pb²⁺, respectively. Therefore, the DNM biosensor capable of simultaneously detecting multiple heavy metal ions with sensitivity and selectivity shows great potential to be point-of-test devices.

PCR-Free Colorimetric DNA Hybridization Detection Using a 3D DNA Nanostructured Reporter Probe

A "sandwich-like" biosensor was developed on the basis of the magnetic bead platform for sensitive detection of breast cancer 1 (BRCA1) DNA. In the present study, a tetrahedron-structured reporter probe (TSRP) was designed, in which 3 vertices of the tetrahedron were labeled with digoxin (Dig), and the other one was labeled with a detection probe. TSRP here provided accurate enzyme loading and well-organized spatial arrangement for optimized signal amplification. The detection limit of this biosensor was as low as 10 fM, which is at least 4 orders of magnitude lower than that of the single DNA probe (100 pM), and the signal gain was 2 times higher than the analysis using three one-dimensional (1D) reporter probes. We could distinguish DNA sequences with only 1 base mismatch, and the performance of our TSRP biosensor was proven to be equally good in both PCR products and real fetal calf serum (FCS) sample as in buffer. We believe this work provided a novel avenue for the development of signal amplification strategies.

Real-Time Continuous Identification of Greenhouse Plant Pathogens Based on Recyclable Microfluidic Bioassay System

The development of a real-time continuous analytical platform for the pathogen detection is of great scientific importance for achieving better disease control and prevention. In this work, we report a rapid and recyclable microfluidic bioassay system constructed from oligonucleotide arrays for selective and sensitive continuous identification of DNA targets of fungal pathogens. We employ the thermal denaturation method to effectively regenerate the oligonucleotide arrays for multiple sample detection, which could considerably reduce the screening effort and costs. The combination of thermal denaturation and laser-induced fluorescence detection technique enables real-time continuous identification of multiple samples (<10 min per sample). As a proof of concept, we have demonstrated that two DNA targets of fungal pathogens (Botrytis cinerea and Didymella bryoniae) can be sequentially analyzed using our rapid microfluidic bioassay system, which provides a new paradigm in the design of microfluidic bioassay system and will be valuable for chemical and biomedical analysis.