Immobilization-free and label-free electrochemical DNA biosensing based on target-stimulated release of redox reporter and its catalytic redox recycling

Herein, we demonstrate a simple, homogenous and label-free electrochemical biosensing system for sensitive nucleic acid detection based on target-responsive porous materials and nuclease-triggered target recycling amplification. The Fe(CN)63- reporter was firstly sealed into the pores of Fe3O4 nanoparticles by probe DNA. Target DNA recognition triggered the controllable release of Fe(CN)63- for the redox reaction with the electron mediator of methylene blue enriched in the dodecanethiol assembled electrode and thereby generating electrochemical signal. The exonuclease III (Exo III)-assisted target recycling and the catalytic redox recycling between Fe(CN)63- and methylene blue contributed for the enhanced signal response toward target recognition. The low detection limit toward target was obtained as 478 fM and 1.6 pM, respectively, by square wave voltammetry and cyclic voltammetry methods. It also possessed a well-discrimination ability toward mismatched strands and high tolerance to complex sample matrix. The coupling of bio-gated porous nanoparticles, nuclease-assisted target amplification and catalytic redox recycling afforded the sensing system with well-controllable signal responses, sensitive and selective DNA detection, and good stability, reusability and reproducibility. It thus opens a new avenue toward the development of simple but sensitive electrochemical biosensing platform.

Direct Detection of Viral Infections from Swab Samples by Probe-Gated Silica Nanoparticle-Based Lateral Flow Assay

Point-of-care diagnosis is crucial to control the spreading of viral infections. Here, universal-modifiable probe-gated silica nanoparticles (SNPs) based lateral flow assay (LFA) is developed in the interest of the rapid and early detection of viral infections. The most superior advantage of the rapid assay is its utility in detecting various sides of the virus directly from the human swab samples and its adaptability to detect various types of viruses. For this purpose, a high concentration of fluorescein and rhodamine B as a reporting material was loaded into SNPs with excellent loading capacity and measured using standard curve, 4.19 μmol ⋅ g-1 and 1.23 μmol ⋅ g-1 , respectively. As a model organism, severe acute respiratory syndrome coronavirus-2 (CoV-2) infections were selected by targeting its nonstructural (NSP9, NSP12) and envelope (E) genes as target sites of the virus. We showed that NSP12-gated SNPs-based LFA significantly outperformed detection of viral infection in 15 minutes from 0.73 pg ⋅ mL-1 synthetic viral solution and with a dilution of 1 : 103 of unprocessed human samples with an increasing test line intensity compared to steady state (n=12). Compared to the RT-qPCR method, the sensitivity, specificity, and accuracy of NSP12-gated SNPs were calculated as 100 %, 83 %, and 92 %, respectively. Finally, this modifiable nanoparticle system is a high-performance sensing technique that could take advantage of upcoming point-of-care testing markets for viral infection detections.

CRISPR/Cas12a-Powered EC/FL Dual-Mode Controlled-Release Homogeneous Biosensor for Ultrasensitive and Cross-Validated Detection of Messenger Ribonucleic Acid

Accurate detection of cancer-associated mRNAs is beneficial to early diagnosis and potential treatment of cancer. Herein, for the first time, we developed a novel CRISPR/Cas12a-powered electrochemical/fluorescent (EC/FL) dual-mode controlled-release homogeneous biosensor for mRNA detection. A functionalized ssDNA P2-capped Fe3O4-NH2 loaded with methylene blue (P2@MB-Fe3O4-NH2) was synthesized as the signal probe, while survivin mRNA was chosen as the target RNA. In the presence of the target mRNA, the nicking endonuclease-mediated rolling circle amplification (NEM-RCA) was triggered to produce significant amounts of ssDNA, activating the collateral activity of Cas12a toward the surrounding single-stranded DNA. Thus, the ssDNA P1 completely complementary to ssDNA P2 was cleaved, resulting in that the ssDNA P2 bio-gate on Fe3O4-NH2 could not be opened due to electrostatic interactions. As a result, there was no or only a little MB in the supernatant after magnetic separation, and the measured EC/FL signal was exceedingly weak. On the contrary, the ssDNA P2 bio-gate was opened, enabling MB to be released into the supernatant, and generating an obvious EC/FL signal. Benefiting from the accuracy of EC/FL dual-mode cross-verification, high amplification efficiency, high specificity of NEM-RCA and CRISPR/Cas12a, and high loading of mesoporous Fe3O4-NH2 on signal molecules, the strategy shows aM-level sensitivity and single-base mismatch specificity. More importantly, the practical applicability of this dual-mode strategy was confirmed by mRNA quantification in complex serum environments and tumor cell lysates, providing a new way for developing a powerful disease diagnosis tool.

Target-Responsive Smart Nanomaterials via a Au-S Binding Encapsulation Strategy for Electrochemical/Colorimetric Dual-Mode Paper-Based Analytical Devices

Target-responsive nanomaterials attract growing interest in the application of drug delivery, bioimaging, and sensing due to the responsive releasing of guest molecules by the smart molecule gate. However, it remains a challenge to develop smart nanomaterials with simple assembly and low nonspecific leakage starting from encapsulation strategies, especially in the sensing field. Herein, Au nanoclusters (Au NCs) were first grown on porous carbon derived from ZIF-8 (PCZIF) to be employed as nanocarriers. By employing the Au NCs as linkers and aptamer (Apta) double-strand hybrids (target Apta and SH-complementary DNA) as capping units, we reported the novel target-responsive nanomaterials of Apta/Au NCs-PCZIF/hemin through Au-S binding encapsulation for sensing assays. The Au-S binding encapsulation strategy simplified the packaging procedure and reduced non-target responsive leakage. As a proof, ochratoxin A (OTA) as a model target participates in the double-strand hybrid competitive displacement reaction and triggered Apta conformation switches from a coil to a G-quadruplex structure accompanied by the dissociation of the gatekeeper. Simultaneously, the released hemin can initiate a self-assembly to form G-quadruplex/hemin DNAzyme. Interestingly, owing to DNAzyme providing electron transfer mediators and peroxidase-like activity, we proposed an electrochemical/colorimetric dual-mode paper-based analytical device (PAD) that provided self-verification to enhance reliability and accuracy, benefiting from independent signal conversion and transmission mechanism. As a consequence, the proposed dual-mode PAD could achieve sensitive electrochemical detection and visual prediction of OTA in the range of 1 pg/mL to 500 ng/mL and 50 pg/mL to 500 ng/mL, respectively. The electrochemical detection limit for OTA was as low as 0.347 pg/mL (S/N = 3). We believe that this work provides point-of-care testing (POCT) tools for a broad spectrum of applications.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Recent advances of functional nucleic acids-based electrochemiluminescent sensing

Electroluminescence (ECL) has been used in extensive applications ranging from bioanalysis to clinical diagnosis owing to its simple device requirement, low background, high sensitivity, and wide dynamic range. Nucleic acid is a significant theme in ECL bioanalysis. The inherent versatile selective molecular recognition of nucleic acids and their programmable self-assembly make it desirable for the robust construction of nanostructures. Benefiting from their unique structures and physiochemical properties, ECL biosensing based on nucleic acids has experienced rapid growth. This review focuses on recent applications of nucleic acids in ECL sensing systems, particularly concerning the employment of nucleic acids as molecular recognition elements, signal amplification units, and sensing interface schemes. In the end, an outlook of nucleic acid-based ECL biosensing will be provided for future developments and directions. We envision that nucleic acids, which act as an essential component for both bioanalysis and clinical diagnosis, will provide a new thinking model and driving force for developing next-generation sensing systems.

Dual-Modular Aptasensor for Detection of Cardiac Troponin I Based on Mesoporous Silica Films by Electrochemiluminescence/Electrochemical Impedance Spectroscopy

A simple, dual-modular aptasensor for accurate determination of cardiac troponin I (cTnI), a sensitive biomarker of acute myocardial infarction, is reported. It has the parallel output of electrochemiluminescence (ECL) and electrochemical impedance spectroscopy (EIS) based on target-gated transportation of signal probes (luminol/H₂O₂ or Fe(CN)₆^3-/4-). The sensing capacity is originated from the amino-functionalized mouth margin of the nanochannels in a vertically oriented mesoporous silica film, which was in situ-grown on indium tin oxide-coated glass. With the linkage of glutaraldehyde to couple the aptamer as a trapper, it brings in the high specific target-gated response toward cTnI as decreased ECL or increased EIS. The concentration of cTnI is measurable by the ECL response within a wide linear range from 0.05 pg mL^-1 to 10 ng mL^-1, as well as the EIS response for a linear range between 0.05 pg mL^-1 and 1 ng mL^-1. Significantly, the self-verification of these two data from ECL and EIS validated each other with a satisfactory linear correlation (R² = 0.999), thereby realizing the more reliable and accurate quantification to avoid false results. The designed strategy is an effective method for detection of cTnI, which is of great potential to apply in clinical detection.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

Toward early cancer detection: Focus on biosensing systems and biosensors for an anti-apoptotic protein survivin and survivin mRNA

The development of biosensors for cancer biomarkers has recently been expanding rapidly, offering promising biomedical applications of these sensors as highly sensitive, selective, and inexpensive bioanalytical tools that can provide alternative methodology to that afforded by the advanced hyphenated-instrumental techniques. In this review, we focus particularly on the detection of a member of the inhibitor of apoptosis proteins (IAP) family, protein survivin (Sur), a ubiquitous re-organizer of the cell life cycle with the ability to inhibit the apoptosis and induce an enhanced proliferation leading to the unimpeded cancer growth and metastasis. Herein, we critically evaluate the progress in the development of novel biosensing systems and biosensors for the detection of two survivin (Sur) biomarkers: the Sur protein and its messenger RNA (Sur mRNA), including immunosensors, electrochemical piezo- and impedance-sensors, electrochemi-luminescence biosensors, genosensors based on oligonucleotide molecular beacons (MBs) with fluorescent or electrochemical transduction, as well as the microfluidic and related analytical platforms based on solution chemistry. The in-situ applications of survivin biomarkers' detection technologies to equip nanocarriers of the controlled drug delivery systems with MB-based fluorescence imaging capability, apoptosis control, and mitigation of the acquired drug resistance are also presented and critically evaluated. Finally, we turn the attention to the application of biosensors for the analysis of Sur biomarkers in exosomes and circulating tumor cells for a non-invasive liquid biopsy. The prospect of a widespread screening for early cancers, based on inexpensive point-of-care testing using biosensors and multiplex biosensor arrays, as a means of reducing the high cancer fatality rate, is discussed.

Paper based modification-free photoelectrochemical sensing platform with single-crystalline aloe like TiO2 as electron transporting material for cTnI detection

By controlling target-induced signal quencher release, a label-free and modification-free microfluidic paper based photoelectrochemical analytical device (μ-PAD) for cardiac troponin-I (cTnI) detection was designed for the first time. To achieve it, cellulose paper based single-crystalline three-dimensional aloe like TiO₂ arrays (PSATs) were firstly fabricated as the electron transporting material, providing direct pathways for the charge carriers transfer, and subsequently coupled with CdS to form PSATs/CdS heterojunction for extending the solar spectrum response. Meanwhile, positive charged mesoporous silica nanoparticles (PMSNs) were prepared as the nanocarrier to efficient entrap the Cu²⁺ which could be regarded as signal quencher due to their reaction with CdS to form Cu_xS. Single stranded DNAs (ssDNAs), which could bind specifically with the target of cTnI, were then introduced to couple with the PMSNs and used as the bio-gate to encapsulate the signal quencher of Cu²⁺, endowing the functional PMSNs with responsiveness to cTnI. When the cTnI existed, the ssDNAs were dissociated from PMSNs due to the formation of cTnI-ssDNAs complexes, triggering controllable release of the trapped Cu²⁺, and further decreasing the photocurrent signal caused by the formation of Cu_xS. Accordingly, the concentration of cTnI could be accurately quantified via the photocurrent, realizing the target-induced modification-free μ-PAD assay. We believe this work could provide an ingenious idea to construct the easy-to-use novel modification-free μ-PAD.

Highly Sensitive Detection of MicroRNA-21 with ICPMS via Hybridization Accumulation of Upconversion Nanoparticles

A highly sensitive platform is developed for the determination of microRNA-21 (miRNA-21) with inductively coupled plasma mass spectrometry (ICPMS). It includes the following operations: Hairpin structures DNA H1 and H2 are designed, and DNA H1 is bound to ultrasmall lanthanide upconversion nanoparticles (UCNPs) to produce UCNPs@DNA conjugate probes. Target miRNA triggers a chain reaction for alternating hybridization between DNA H1 (bound on UCNPs@DNA probe) and DNA H2. This leads to UCNPs accumulation and serves as an efficient amplification strategy for UCNPs. The concentration of miRNA-21 is closely correlated to the number of UCNPs; thus, the detection of ⁸⁹Y by ICPMS provides a promising approach for miRNA quantification. This protocol exhibits high sensitivity to miRNA-21 within 0.1-500 fM, along with a detection limit of 41 aM, which is among the hitherto reported most sensitive procedures. It is worth mentioning that rare earth elements are scarcely present in living systems, which minimizes the background for ICPMS detection and excludes potential interferences from the coexisting species, which is most suited for biological assay.

Integration of Biofuel Cell-Based Self-Powered Biosensing and Homogeneous Electrochemical Strategy for Ultrasensitive and Easy-To-Use Bioassays of MicroRNA

Biofuel cell (BFC)-based self-powered biosensors have attracted substantial attentions because of their unique merits such as having no need for power sources (only two electrodes are needed). More importantly, in case it can also work in a homogeneous system, more efficient and easy-to-use bioassays could come true. Thus, herein, we proposed a novel homogeneous self-powered biosensing strategy via the integration of BFCs and a homogeneous electrochemical method, which was further utilized for ultrasensitive microRNA (miRNA) detection. To construct such an assay protocol, the cathodic electron acceptor [Fe(CN)₆]^3- was entrapped in the pores of positively charged mesoporous silica nanoparticles and capped by the biogate DNAs. Once the target miRNA existed, it would trigger the controlled release of [Fe(CN)₆]^3-, leading to the dramatic increase of the open circuit voltage. Consequently, the "signal-on" homogeneous self-powered biosensor for the ultrasensitive miRNA assay was realized. Encouragingly, the limit of detection for the miRNA-21 assay was down to 2.7 aM (S/N = 3), obviously superior to those of other analogous reported approaches. This work not only provides an ingenious idea to construct the ultrasensitive and easy-to-use bioassays of miRNA but also exhibits a successful prototype of a portable and on-site biomedical sensor.

An electrochemiluminescence biosensor for Kras mutations based on locked nucleic acid functionalized DNA walkers and hyperbranched rolling circle amplification

Herein, an electrochemiluminescence (ECL) biosensor for ultrasensitive and specific detection of Kras mutant genes has been developed on the basis of the high discrimination capability of locked nucleic acid (LNA) and dual signal amplification techniques including DNA walkers and hyperbranched rolling circle amplification (HRCA).

Recent applications of the combination of mesoporous silica nanoparticles with nucleic acids: development of bioresponsive devices, carriers and sensors

The discovery and control of the biological roles mediated by nucleic acids have turned them into a powerful tool for the development of advanced biotechnological materials. Such is the importance of these gene-keeping biomacromolecules that even nanomaterials have succumbed to the claimed benefits of DNA and RNA. Currently, there could be found in the literature a practically intractable number of examples reporting the use of combination of nanoparticles with nucleic acids, so boundaries are demanded. Following this premise, this review will only cover the most recent and powerful strategies developed to exploit the possibilities of nucleic acids as biotechnological materials when in combination with mesoporous silica nanoparticles. The extensive research done on nucleic acids has significantly incremented the technological possibilities for those biomacromolecules, which could be employed in many different applications, where substrate or sequence recognition or modulation of biological pathways due to its coding role in living cells are the most promising. In the present review, the chosen counterpart, mesoporous silica nanoparticles, also with unique properties, became a reference material for drug delivery and biomedical applications due to their high biocompatibility and porous structure suitable for hosting and delivering small molecules. Although most of the reviews dealt with significant advances in the use of nucleic acid and mesoporous silica nanoparticles in biotechnological applications, a rational classification of these new generation hybrid materials is still uncovered. In this review, there will be covered promising strategies for the development of living cell and biological sensors, DNA-based molecular gates with targeting, transfection or silencing properties, which could provide a significant advance in current nanomedicine.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

A single-cell analysis platform for electrochemiluminescent detection of platelets adhesion to endothelial cells based on Au@DL-ZnCQDs nanoprobes

A novel single-cell analysis platform (SCA) was developed for the investigation of platelets adhesion to single human umbilical vein endothelial cell (HUVEC) via using the adhesion molecule (E-selectin) on the damaged HUVEC as the marker site, and integrating electrochemiluminescence (ECL) with the ultrasensitive Au@DL-ZnCQDs nanoprobes. The Au@DL-ZnCQDs nanocomposite, a kind of double layer zinc-coadsorbed carbon quantum dot (ZnCQDs) core-shell nanoprobe, was firstly constructed by using gold nanoparticles (AuNPs) as the core to load with ZnCQDs and then the citrate-modified silver nanoparticles (AgNPs) as the bridge to link AuNPs-ZnCQDs with ZnCQDs to form the core-shell with double layer ZnCQDs (DL-ZnCQDs) nanoprobe, revealed a 10-fold signal amplification. The H₂O₂-induced oxidative damage HUVECs were utilized as the cellular model on which anti-E-selectin functionalized nanoprobes specially recognized E-selectin, the SCA showed that the ECL signals decreased with platelets adhesion to single HUVEC. The proposed SCA could effectively and dynamically monitor the adhesion between single HUVEC and platelets in the absence and presence of collagen activation, moreover, be able to quantitatively detect the number of platelets adhesion to single HUVEC, and show a good analytical performance with linear range from 1 to 15 platelets. In contrast, the HUVEC was down-regulated the expression of adhesion molecules by treating with quercetin inhibitor, and the SCA also exhibited the feasibility for analysis of platelets adhesion to single HUVEC. Therefore, the single-cell analysis platform provided a novel and promising protocol for analysis of the single intercellular adhesion, and it will be beneficial to elucidate the pathogenesis of cardiovascular diseases.

Nanopore biosensor for sensitive and label-free nucleic acid detection based on hybridization chain reaction amplification

A label-free nanopore biosensor for detection of DNA target is proposed utilizing hybridization chain reaction (HCR) strategy for signal amplification. The DNA target triggered HCR to form large DNA nanostructure inside the nanopore and out the nanopore membrane, which inducing the ionic current decrease effectively due to the blockage of the nanopore. The developed method achieves a desirable sensitivity of 30fM with a wide linear dynamic range from 0.1 to 10pM and demonstrated good application for real sample analysis. This work has great potential to be applied in the early diagnosis of gene-related diseases and provide a new paradigm for label-free nucleic acid amplification strategy in ultrasensitive nanopore biosensor.

Novel Single-Cell Analysis Platform Based on a Solid-State Zinc-Coadsorbed Carbon Quantum Dots Electrochemiluminescence Probe for the Evaluation of CD44 Expression on Breast Cancer Cells

A novel single-cell analysis platform was fabricated using solid-state zinc-coadsorbed carbon quantum dot (ZnCQDs) nanocomposites as an electrochemiluminescence (ECL) probe for the detection of breast cancer cells and evaluation of the CD44 expression level. Solid-state ZnCQDs nanocomposite probes were constructed through the attachment of ZnCQDs to gold nanoparticles and then the loading of magnetic beads to amplify the ECL signal, exhibiting a remarkable 120-fold enhancement of the ECL intensity. Hyaluronic acid (HA)-functionalized solid-state probes were used to label a single breast cancer cell by the specific recognition of HA with CD44 on the cell surface, revealing more stable, sensitive, and effective tagging in comparison with the water-soluble CQDs. This strategy exhibited a good analytical performance for the analysis of MDA-MB-231 and MCF-7 single cells with linear range from 1 to 18 and from 1 to 12 cells, respectively. Furthermore, this single-cell analysis platform was used for evaluation of the CD44 expression level of these two cell lines, in which the MDA-MB-231 cells revealed a 2.8-5.2-fold higher CD44 expression level. A total of 20 single cells were analyzed individually, and the distributions of the ECL intensity revealed larger variations, indicating the high cellular heterogeneity of the CD44 expression level on the same cell line. The as-proposed single-cell analysis platform might provide a novel protocol to effectively study the individual cellular function and cellular heterogeneity.

Monitoring of “on-demand” drug release using dual tumor marker mediated DNA-capped versatile mesoporous silica nanoparticles

We constructed a versatile drug delivery system using dual internal stimulus, achieving controllable release and monitoring simultaneously.

A water-stable metal–organic framework of a zwitterionic carboxylate with dysprosium: a sensing platform for Ebolavirus RNA sequences

A 3D Dy-based metal–organic framework (MOF) 1 was synthesized. Compound 1 can interact with the probe DNA to form a P-DNA@1 system. This system can be used as an effective fluorescent sensing platform for the detection of Ebolavirus RNA.