Self-Assembled DNA Tetrahedral Scaffolds for the Construction of Electrochemiluminescence Biosensor with Programmable DNA Cyclic Amplification

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.

Recent Advances in Nanomaterials Based Optical Sensors for the Detection of Melatonin and Serotonin

In this review paper we discussed the detection of melatonin and serotonin by using various optical methods. Melatonin and serotonin are very necessary body hormones these are also called neuroregulatory hormones secreted by pineal gland in brain by pinealocytes and shape of pineal gland is cone like. Sensitive detection of melatonin and serotonin in pharmacological samples and human serum is crucial for human beings, lots of research publications available in literature for melatonin and serotonin and we overviewed these papers. We have deeply reviewed many research papers where sensitively sensing of melatonin and serotonin occurs, by using of various interfering agents and nanomaterials. This review aims presenting colorimetry, fluorometry and spectrophotometric detection of melatonin (MEL) and serotonin (SER) by using different metal oxides, carbon nanomaterials (nanosheets, nanorods, nanofibers) and many other agents. Nanomaterials typically possess favourable optical, electrical and mechanical characteristics, they provide up new avenues for enhancing the efficacy of sensors. It is crucial to provide an optical sensors platform that is dependable, sensitive and low price. The development of sensors and biosensors to use nanomaterials for neurotransmitters has advanced significantly in recent years. There are currently many developing biomarkers in biological fluids, and bionanomaterial-based biosensor systems, as well as clinical and pharmacological settings, have garnered significant interest. Biomarkers have been found using optical devices in a quick, selective and sensitive manner. Our aim is to compile all the data that already published on MEL, SER sensing and comparison of each method, we mainly focused on principle, observations, sensitivity, selectivity, limit of detection, mechanism behind the reaction, effect of temperature, pH and concentration. In the last of this paper, we discuss some challenges of these methods and future projects.

A novel paper-based electrochemiluminescence biosensor for non-destructive detection of pathogenic bacteria in real samples

The demand for sensitive, portable, and non-destructive analysis of pathogenic bacteria is of significance in point-of-care diagnosis. Herein, we constructed a smart electrochemiluminescence (ECL) biosensor by integrating a flexible paper-based sensing device and a disposable three-electrode detecting system. Staphylococcus aureus (S. aureus)-responsive cellulose paper was prepared by employing aptamer as recognition element and a probe DNA (probe DNA-GOD) tagged with glucose oxidase (GOD) as a signal amplification unit. The formation of aptamer-S. aureus complex mediated the quantitative release of probe DNA-GOD. The remaining probe DNA-GOD on the paper-based aptasensor was then activated by glucose, which resulted in a significant decrease in ECL signal. To further improve the ECL performance of biosensor, a large number of Ru(bpy)32+ molecules were embedded into porous zinc-based metal-organic frameworks (MOFs) to form Ru(bpy)32+ functionalized MOF nanoflowers (Ru-MOF-5 NFs). Such biosensor enabled accurate, non-destructive, and real-time monitoring of S. aureus-contaminated food samples, opening a new avenue for sensitive recognition of pathogenic bacteria.

Development of a regenerable dual-trigger tripedal DNA walker electrochemical biosensor for sensitive detection of microRNA-155

Since microRNAs (miRNAs) are valuable biomarkers for disease diagnosis and prognosis, the pursuit of enhanced detection sensitivity through signal amplification strategies has emerged as a prominent focus in low-abundance miRNA detection research. DNA walkers, as dynamic DNA nanodevice, have gained significant attention for their applications as signal amplification strategies. To overcome the limitations of unipedal DNA walkers with a restricted signal amplification efficiency, there is a great need for multi-pedal DNA walkers that offer improved walking and signal amplification capabilities. Here, we employed a combination of catalytic hairpin assembly (CHA) and APE1 enzymatic cleavage reactions to construct a tripedal DNA walker, driving its movement to establish a cascade signal amplification system for the electrochemical detection of miRNA-155. The biosensor utilizes tumor cell-endogenous microRNA-155 and APE1 as dual-trigger for DNA walker formation and walking movement, leading to highly efficient and controllable signal amplification. The biosensor exhibited high sensitivity, with a low detection limit of 10 pM for microRNA-155, and successfully differentiated and selectively detected microRNA-155 from other interfering RNAs. Successful detection in 20 % serum samples indicates its potential clinical application. In addition, we harnessed strand displacement reactions to create a gentle yet efficient electrode regeneration strategy, to addresses the time-consuming challenges during electrode modification processes. We have successfully demonstrated the stability of current signals even after multiple cycles of electrode regeneration. This study showcased the high-efficiency amplification potential of multi-pedal DNA walkers and the effectiveness and versatility of strand displacement in biosensing applications. It opens a promising path for developing regenerable electrochemical biosensors. This regenerable strategy for electrochemical biosensors is both label-free and cost-effective, and holds promise for detecting various disease-related RNA targets beyond its current application.

Electrochemiluminescent CdS Quantum Dots Biosensor for Cancer Mutation Detection at Different Positions on Linear DNA Analytes

PCR-based techniques routinely employed for the detection of mutated linear DNA molecules, including circulating tumor DNA (ctDNA), require large nucleotide sections on both sides of the mutation for primer annealing. This means that DNA fragments with a mutation positioned closer to the extremities are unlikely to be detected. Thus, sensors capable of recognizing linear DNA with characteristic mutations closer to the ends would be advantageous over the state-of-the-art approaches. Here, an electrochemiluminescence-resonance energy transfer (ECL-RET) biosensor comprising capped CdS quantum dots and hairpin DNA probes labeled with Au nanoparticles was developed for the detection of epidermal growth factor receptor (EGFR) ctDNA carrying the critical T790M lung cancer mutation. The ECL-RET system detected different DNA molecules including single-stranded 18-nucleotides (nt) and 40-nt as well as double-stranded 100-nt with the single nucleotide polymorphism (SNP) coding for T790M located either in the middle or only 7 nt from one end. For all target DNA, the sensor's limits of detection (LODs) were in the aM range, with excellent selectivity. It was the case of 100-nt target linear ctDNA fragments with LODs of 8.1 and 3.4 aM when the EGFR T790M SNP was either in the middle or at the end, respectively. These results show that ECL-RET systems can sense mutations in DNA fragments that would remain undetected by standard techniques.

CuS quantum dots activated DNAzyme for ratiometric electrochemical detection of telomerase activity

Telomerase activity detection has attracted much attention concerning its importance for early cancer diagnosis. Here, we established a ratiometric electrochemical biosensor for telomerase detection based on CuS quantum dots (CuS QDs) dependent DNAzyme-regulated dual signals. The telomerase substrate probe was used as the linker to combine the DNA fabricated magnetic beads and CuS QDs. In this way, telomerase extended the substrate probe with repeated sequence to from hairpin structure, releasing CuS QDs as an input to DNAzyme modified electrode. DNAzyme was cleaved with high current of ferrocene (Fc) and low current of methylene blue (MB). On the basis of the obtained ratiometric signals, telomerase activity detection was achieved in the range of 1.0 × 10^-12-1.0 × 10^-6 IU/L, with the limit of detection down to 2.75 × 10^-14 IU/L. Moreover, telomerase activity from HeLa extracts was also tested to verify the clinical application.

Strategies for Enhancing the Sensitivity of Electrochemiluminescence Biosensors

Electrochemiluminescence (ECL) has received considerable attention as a powerful analytical technique for the sensitive and accurate detection of biological analytes owing to its high sensitivity and selectivity and wide dynamic range. To satisfy the growing demand for ultrasensitive analysis techniques with high efficiency and accuracy in complex real sample matrices, considerable efforts have been dedicated to developing ECL strategies to improve the sensitivity of bioanalysis. As one of the most effective approaches, diverse signal amplification strategies have been integrated with ECL biosensors to achieve desirable analytical performance. This review summarizes the recent advances in ECL biosensing based on various signal amplification strategies, including DNA-assisted amplification strategies, efficient ECL luminophores, surface-enhanced electrochemiluminescence, and ratiometric strategies. Sensitivity-enhancing strategies and bio-related applications are discussed in detail. Moreover, the future trends and challenges of ECL biosensors are discussed.

Signal Transduction Strategies for Analyte Detection Using DNA-Based Nanostructures

The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures. The utility of these structures arises both from DNA's inherent ability to selectively recognize and bind a variety of chemical species and from the unique properties observed when DNA is restructured at the nanoscale. In this Minireview, we chronicle the most commonly used signal transduction strategies that have been interfaced with various DNA-based nanostructures. We discuss the types of analytes and the detection scenarios that are sought after, delineate the advantages and disadvantages of each signaling strategy, and outline the key considerations that guide the selection of each signaling method.

Enzyme-free nucleic acid dual-amplification strategy combined with mimic enzyme catalytic precipitation reaction for the photoelectrochemical detection of microRNA-21

A novel photoelectrochemical (PEC) biosensor based on an enzyme-free nucleic acid dual-amplification strategy combined with a mimic enzyme to catalyze the deposition of a quencher is reported for the ultrasensitive detection of miRNA-21. A limited amount of target miRNA-21 can trigger the formation of long DNA duplexes on the electrode, owing to the synergistic effect of the enzyme-free nucleic acid dual-amplification strategy of entropy-driven strand displacement reaction (ESDR) amplification and hybridization chain reaction (HCR) amplification. The embedded manganese porphyrin (MnPP) in the long DNA duplexes acts as a horseradish peroxidase (HRP)-mimicking enzyme to catalyze the transformation of benzo-4-chlorohexadienone on the electrode surface, resulting in a significant reduction in photocurrent intensity. As a photosensitive material, BiOCl-BiOI is used as a tag to provide strong initial PEC signals. Based on the cascade integration of the enzyme-free nucleic acid dual-amplification strategy and the mimic enzyme-catalyzed precipitation reaction, the current PEC biosensor exhibits outstanding performance for miRNA-21 detection with an ultralow detection limit (33 aM) and a wide quantification range (from 100 aM to 1 nM). This work provides a new avenue toward the ultrasensitive detection of miRNAs, and is expected to be used for clinical and biochemical samples. A unique PEC biosensor with the BiOCl-BiOI composite, as the photosensitive material, has been developed for ultrasensitive miRNA-21 determination based on the combination of an enzyme-free nucleic acid dual-amplification strategy and mimic enzyme catalytic precipitation reaction.

Shared-cathode closed bipolar electrochemiluminescence cloth-based chip for multiplex detection

Electrochemiluminescence (ECL) chips have been widely used in the field of medical diagnosis. However, most of these chips currently in use are costly and require high amounts of sample. In this work, we present, for the first time, a shared-cathode closed bipolar electrochemiluminescence (SC-CBP-ECL) cloth-based chip, which can be used for multiplex detection. The SC-CBP-ECL chips ($0.03-0.05 for each chip) are manufactured using carbon ink- and wax-based screen-printing techniques, without the need for expensive and complex fabrication equipment. Under optimised conditions, the SC-CBP-ECL chips were successfully used for coinstantaneous detection of glucose in double ECL systems (i.e., Ru(bpy)₃²⁺ and luminol), with corresponding linear ranges of 0.05-1 mM and 0.05-10 mM, and detection limits of 0.0382 mM and 0.0422 mM. To our knowledge, this is the first report on the application of fibre material-based closed bipolar electrodes (C-BPE) combined with double ECL systems. Furthermore, the SC-CBP-ECL chips exhibit an acceptable specificity and good reproducibility and stability and can be used for glucose detection in human serum samples with a good agreement compared with the clinical method. Finally, the SC-CBP-ECL chips could be successfully used for simultaneous detection of seven glucose samples and also show potential for simultaneous detection of three different targets (hydrogen peroxide [H₂O₂], glucose, and uric acid [UA]). Therefore, we believe that the chip described in this study has broad potential application in the field of cost-effective multiplex detection.

A dual-mechanism-driven electrochemiluminescence aptasensor for sensitive detection of β-amyloid peptides

β-Amyloid (Aβ) peptides can bind both Cu²⁺ and heme cofactors simultaneously to form heme-Cu²⁺-Aβ complexes, which are proposed to generate toxic partially reduced oxygen species (PROS, e.g., H₂O₂) and play a vital role in Alzheimer's disease (AD). In this paper, a competitive dual-mechanism-driven electrochemiluminescence (ECL) aptasensor integrating the synergistic enhancement and steric hindrance effect was described for Aβ detection. Specifically, graphite carbon nitride (g-C₃N₄) as an effective ECL luminescent substrate and Au nanoparticles were sequentially assembled on the Au electrode surface, and then a thiol-modified aptamer for capturing Aβ peptide was attached to the surface of the electrode through the Au-S bond. Aβ peptides were simultaneously incubated with heme and Cu²⁺, and the forming heme-Cu²⁺-Aβ complexes were subsequently anchored on the electrode through the specific recognition between the target Aβ and the aptamer. When the concentration of the target Aβ is low, the synergistic enhancement effect arising from K₂S₂O₈ with in situ generated H₂O₂ is predominant, resulting in an increase in the ECL signal of g-C₃N₄. In contrast, when the concentration of Aβ is high, the steric hindrance effect generated from heme-Cu²⁺-Aβ complexes is dominant, leading to a decrease in the ECL signal. The present sensor exhibits a favorable linear response for the detection of Aβ with a relatively low detection limit of 0.24 pM, and provides a more sensitive and selective platform for bioanalysis.

Antisense technology as a potential strategy for the treatment of coronaviruses infection: With focus on COVID-19

After the outbreak of coronavirus disease 2019 (COVID-19) in December 2019 and the increasing number of SARS-CoV-2 infections all over the world, researchers are struggling to investigate effective therapeutic strategies for the treatment of this infection. Targeting viral small molecules that are involved in the process of infection is a promising strategy. Since many host factors are also used by SARS-CoV-2 during various stages of infection, down-regulating or silencing these factors can serve as an effective therapeutic tool. Several nucleic acid-based technologies including short interfering RNAs, antisense oligonucleotides, aptamers, DNAzymes, and ribozymes have been suggested for the control of SARS-CoV-2 as well as other respiratory viruses. The antisense technology also plays an indispensable role in the treatment of many other diseases including cancer, influenza, and acquired immunodeficiency syndrome. In this review, we summarised the potential applications of antisense technology for the treatment of coronaviruses and specifically COVID-19 infection.

An in situ quenching electrochemiluminescence biosensor amplified with aptamer recognition-induced multi-DNA release for sensitive detection of pathogenic bacteria

An in situ quenching electrochemiluminescence (ECL) biosensor sensitized with the aptamer recognition-induced multi-DNA release was designed for pathogenic bacterial detection. Benefitting from the high binding ability of the aptamer to targets and large enrichment capacity of magnetic bead separation, the proposed sensing system not only exhibited outstanding identification to Staphylococcus aureus (S. aureus) among various bacteria, but also released abundant signal transduction DNAs. One S. aureus initiated the dissociation of four kinds of DNA sequences, achieving a one-to-multiple amplification effect. These multi-DNA strands were further hybridized with capture DNA, which were assembled to an electrode modified with Ru(bpy)₃²⁺-conjugated silica nanoparticles (RuSi NPs). Then, glucose oxidase (GOD) was introduced via the functional conjugation of GOD-multi-DNA, leading to the presence of H₂O₂ by in situ catalysis of GOD on glucose. Relying on the ECL quenching of H₂O₂ in the Ru(bpy)₃²⁺ system, S. aureus was quantified with a linear range from 10 to 10⁷ CFU/mL. In addition, the negative results of non-target bacteria and good recovery efficiency in real samples revealed the system's remarkable selectivity and potential application in infectious food tests.

SARS-CoV-2 monitoring by automated target-driven molecular machine-based engineering

Biosensors based on nucleic acid-structured electrochemiluminescence are rapidly developing for medical diagnostics. Here, we build an automated DNA molecular machine on Ti₃C₂/polyethyleneimine-Ru(dcbpy)₃ ²⁺@Au composite, which alters the situation that a DNA molecular machine requires laying down motion tracks. We use this DNA molecular machine to transduce the target concentration information to enhance the electrochemiluminescence signal based on DNA hybridization calculations. Complex bioanalytical processes are centralized in a single nucleic acid probe unit, thus eliminating the tedious steps of laying down motion tracks required by the traditional molecular machine. We found a detection limit of 0.68 pM and a range of 1 pM to 1 nM for the analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific DNA target. Recoveries range between 96.4 and 104.8% for the analysis of SARS-CoV-2 in human saliva.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10311-022-01434-9.

The effect of carbon-based copper nanocomposites on Microcystis aeruginosa and the movability of antibiotic resistance genes in urban water

The presence of Microcystis aeruginosa (M. aeruginosa) can affect the transference of antibiotic resistance genes (ARGs), and the presence of carbon-based copper nanocomposites (CCN) can affect the growth of M. aeruginosa. However, the effect of CCN on M. aeruginosa and ARGs is not fully understood. In this study, metagenomic sequencing was employed to analyze the movability of ARGs, their potential transfer, and possible hosts in photobioreactor treating urban water. The results uggested that 20 mg/L of CCN changed the composition and abundance of microorganisms in urban water, significantly promoted the flocculation of M aeruginosa, and decreased the composing proportion of Cyanophyta sp. and M aeruginosa. The results indicated that 20 mg/L of CCN significantly decreased the absolute abundance and ARGs proportions which mediated by plasmids (32.7 %). Furthermore, the lower co-occurrence probability of ARGs and mobile genetic elements (MGEs) suggested that 20 mg/L of CCN weakened the movability potential of ARGs mediated by MGEs such as plasmids. Among the 452 metagenome-assembled genomes (MAGs), 95 MAGs belonging to 41 bacterial categories were identified as possible ARG hosts. These results will provide insights into the control of harmful cyanobacteria and the management of ARGs in urban water.

Entropy-driven amplified electrochemiluminescence biosensor for RdRp gene of SARS-CoV-2 detection with self-assembled DNA tetrahedron scaffolds

Dependable, specific and rapid diagnostic methods for severe acute respiratory syndrome β-coronavirus (SARS-CoV-2) detection are needed to promote public health interventions for coronavirus disease 2019 (COVID-19). Herein, we have established an entropy-driven amplified electrochemiluminescence (ECL) strategy to detect the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 known as RdRp-COVID which as the target for SARS-CoV-2 plays an essential role in the diagnosis of COVID-19. For the construction of the sensors, DNA tetrahedron (DT) is modified on the surface of the electrode to furnish robust and programmable scaffolds materials, upon which target DNA-participated entropy-driven amplified reaction is efficiently conducted to link the Ru (bpy)32+ modified S3 to the linear ssDNA at the vertex of the tetrahedron and eventually present an "ECL on" state. The rigid tetrahedral structure of the DT probe enhances the ECL intensity and avoids the cross-reactivity between single-stranded DNA, thus increasing the sensitivity of the assays. The enzyme-free entropy-driven reaction prevents the use of expensive enzyme reagents and facilitates the realization of large-scale screening of SARS-CoV-2 patients. Our DT-based ECL sensor has demonstrated significant specificity and high sensitivity for SARS-CoV-2 with a limit of detection (LOD) down to 2.67 fM. Additionally, our operational method has achieved the detection of RdRp-COVID in human serum samples, which supplies a reliable and feasible sensing platform for the clinical bioanalysis.

Zippering DNA Tetrahedral Hyperlink for Ultrasensitive Electrochemical MicroRNA Detection

Pluripotency of a DNA tetrahedron (DNA^TT) has made the iconic framework a compelling keystone in biosensors and biodevices. Herein, distinct from the well-tapped applications in substrate fabrication, we focus on exploring their tracing and signaling potentials. A homologous family of four isostructural DNA^TT, i.e., DNA^{TTα/β/γ/δ}, was engineered to form a sensor circuitry, in which a target-specific monolayer of thiolated DNA^TTγ pinned down the analyte jointly with the reciprocal DNA^TTδ into a sandwich complex; the latter further rallied an in situ interdigital relay of biotinylated DNA^TTα/β into a microsized hyperlink dubbed polyDNA^TT. Its scale and growth factors were illuminated rudimentarily in transmission electron microscopy and confocal laser scanning microscopy. Using a nonsmall-cell lung cancer-related microRNA (hsa-miR-193a-3p) as the subject, a compound DNA-backboned construct was synthesized, fusing all building blocks together. Its superb tacticity and stereochemical conformality avail the templating of a horseradish peroxidase train, which boosted the paralleled catalytic surge of proton donors, resulting in an attomolar detection limit and a broad calibration range of more than seven orders of magnitude. Such oligomerization bested the conventional hybridization chain reaction laddering at both biomechanical stability and stoichiometric congruency. More significantly, it demonstrates the flexibility of DNA architectures and their multitasking ability in biosensing.

DNA Framework-Supported Electrochemical Analysis of DNA Methylation for Prostate Cancers

Epigenetic alterations hold great promise as biomarkers for early stage cancer diagnosis. Nevertheless, direct identification of rare methylated DNA in the genome remains challenging. Here, we report an ultrasensitive framework nucleic acid-based electrochemical sensor for quantitative and highly selective analysis of DNA methylation. Notably, we can detect 160 fg of methylated DNA in million-fold unmethylated DNA samples using this electrochemical methylation-specific polymerase chain reaction (E-MSP) method. The high sensitivity of E-MSP enables one-step detection of low-abundance methylation at two different genes in patient serum samples. By using a combination test with two methylation alterations, we achieve high accuracy and sensitivity for reliable differentiation of prostate cancer and benign prostate hypertrophy (BPH). This new method sheds new light on translational use in early cancer diagnosis and in monitoring patients' responses to therapeutic agents.

Fe-MOFs as signal probes coupling with DNA tetrahedral nanostructures for construction of ratiometric electrochemical aptasensor

A ratiometric electrochemical aptasensor is proposed for the detection of thrombin. In the sensor, the iron metal-organic frameworks (Fe MOFs)-labeled aptamer as signal tags was used as signal probe (SP), and the electrolyte solution [Fe(CN)₆]^3-/4- was utilized as an inner reference probe (IR). In the presence of thrombin, the signal of Fe-MOFs can be detected. Meanwhile, the signal of [Fe(CN)₆]^3-/4_-IR almost remains stable. Accordingly, thrombin concentration can be monitored with the ratio response of I_Fe-MOFs-SP/I_[Fe(CN)6]^3-/4-_-IR. The proposed ratiometric biosensor owns a strong ability to eliminate the disturbance that arises from different DNA loading densities, environmental impact and instrumental efficiency. DNA nanotetrahedron (NTH) with three-dimensional (3D) scaffold can effectively eliminate nonspecific adsorption of DNA and protein. The accessibility of target molecules and loading amounts of signal substances could be increased because of the enhanced mechanical rigidity of well-designed 3D NTH. Thus, detection reproducibility and sensitivity can be further improved. Moreover, the biosensor only requires conjugation with one electroactive substance. The modification procedure can be greatly simplified. The biosensor owns high sensitivity with the detection limit of 59.6 fM. We expect that it will emerge as a generalized ratiometric sensor that may be useful for detecting target analytes.

Ultrasensitive Electrochemical DNA Biosensor Fabrication by Coupling an Integral Multifunctional Zirconia-Reduced Graphene Oxide-Thionine Nanocomposite and Exonuclease I-Assisted Cleavage

In this work, a simple but sensitive electrochemical DNA biosensor for nucleic acid detection was developed by taking advantage of exonuclease (Exo) I-assisted cleavage for background reduction and zirconia-reduced graphene oxide-thionine (ZrO2-rGO-Thi) nanocomposite for integral DNA recognition, signal amplification, and reporting. The ZrO2-rGO nanocomposite was obtained by a one-step hydrothermal synthesis method. Then, thionine was adsorbed onto the rGO surface, via π-π stacking, as an excellent electrochemical probe. The biosensor fabrication is very simple, with probe DNA immobilization and hybridization recognition with the target nucleic acid. Then, the ZrO2-rGO-Thi nanocomposite was captured onto an electrode via the multicoordinative interaction of ZrO2 with the phosphate group on the DNA skeleton. The adsorbed abundant thionine molecules onto the ZrO2-rGO nanocomposite facilitated an amplified electrochemical response related with the target DNA. Since upon the interaction of the ZrO2-rGO-Thi nanocomposite with the probe DNA an immobilized electrode may also occur, an Exo I-assisted cleavage was combined to remove the unhybridized probe DNA for background reduction. With the current proposed strategy, the target DNA related with P53 gene could be sensitively assayed, with a wide linear detection range from 100 fM to 10 nM and an attractive low detection limit of 24 fM. Also, the developed DNA biosensor could differentiate the mismatched targets from complementary target DNA. Therefore, it offers a simple but effective biosensor fabrication strategy and is anticipated to show potential for applications in bioanalysis and medical diagnosis.

DNA framework-engineered electrochemical biosensors

Self-assembled DNA nanostructures have shown remarkable potential in the engineering of biosensing interfaces, which can improve the performance of various biosensors. In particular, by exploiting the structural rigidity and programmability of the framework nucleic acids with high precision, molecular recognition on the electrochemical biosensing interface has been significantly enhanced, leading to the development of highly sensitive and specific biosensors for nucleic acids, small molecules, proteins, and cells. In this review, we summarize recent advances in DNA framework-engineered biosensing interfaces and the application of corresponding electrochemical biosensors.

An aptamer-binding DNA walking machine for sensitive electrochemiluminescence detection of tumor exosomes

An aptamer-binding DNA walking machine triggered by the recognition of aptamers to exosomes was firstly reported for sensitive electrochemiluminescence (ECL) detection of exosomes.

Molecular architectonics of DNA for functional nanoarchitectures

DNA is the key biomolecule central to almost all processes in living organisms. The eccentric idea of utilizing DNA as a material building block in molecular and structural engineering led to the creation of numerous molecular-assembly systems and materials at the nanoscale. The molecular structure of DNA is believed to have evolved over billions of years, with structure and stability optimizations that allow life forms to sustain through the storage and transmission of genetic information with fidelity. The nanoscale structural characteristics of DNA (2 nm thickness and ca. 40-50 nm persistence length) have inspired the creation of numerous functional patterns and architectures through noncovalent conventional and unconventional base pairings as well as through mutual templating-interactions with small organic molecules and metal ions. The recent advancements in structural DNA nanotechnology allowed researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of molecular architectonics enabled the creation of novel DNA nanoarchitectures with potential applications, which has been termed as templated DNA nanotechnology or functional DNA nanoarchitectonics. This review highlights the molecular architectonics-guided design principles and applications of the derived DNA nanoarchitectures. The advantages and ability of functional DNA nanoarchitectonics to overcome the trivial drawbacks of classical DNA nanotechnology to fulfill realistic and practical applications are highlighted, and an outlook on future developments is presented.

Enhanced biosensing strategies using electrogenerated chemiluminescence: recent progress and future prospects

An overview of enhancement strategies for highly sensitive ECL-based sensing of bioanalytes enabling early detection of cancer.

Bioapplications of DNA nanotechnology at the solid-liquid interface

DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.

Recent Advances in Electrochemiluminescence Sensors for Pathogenic Bacteria Detection

Pathogenic bacterial contamination greatly threats human health and safety. Rapidly biosensing pathogens in the early stage of infection would be helpful to choose the correct drug treatment, prevent transmission of pathogens, as well as decrease mortality and economic losses. Traditional techniques, such as polymerase chain reaction and enzyme-linked immunosorbent assay, are accurate and effective, but are greatly limited because they are complex and time-consuming. Electrochemiluminescence (ECL) biosensors combine the advantages of both electrochemical and photoluminescence analysis and are suitable for high sensitivity and simple pathogenic bacteria detection. In this review, we summarize recent advances in ECL sensors for pathogenic bacteria detection and highlight the development of paper-based ECL platforms in point of care diagnosis of pathogens.

A cascade toehold-mediated strand displacement strategy for label-free and sensitive non-enzymatic recycling amplification detection of the HIV-1 gene

In this work, a label-free fluorescence biosensor for simple detection of the HIV-1 gene was proposed by using toehold-mediated strand displacement reactions (TMSDRs) combined with a non-enzymatic target recycling amplification strategy. In this system, two TMSDRs were used. In the presence of the HIV-1 gene, an autocatalytic DNA machine can be activated. This leads to the generation of numerous free G-rich sequences, which can associate with a fluorescent dye N-methylmesoporphyrin IX (NMM) to yield an amplified fluorescence signal for the target detection. This sensing platform showed a high sensitivity towards the HIV-1 gene with a detection limit as low as 1.9 pM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits an excellent selectivity for the HIV-1 gene compared with other interference DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the HIV-1 gene in a real biological sample with satisfactory results, suggesting that this method is promising for simple and early clinical diagnosis of HIV infection. Thanks to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a universal platform for the detection of other genes by substituting the target-recognition element.

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.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

A smart fluorescent biosensor for the highly sensitive detection of BRCA1 based on a 3D DNA walker and ESDR cascade amplification

Nucleic acid analysis plays an important role in the diagnosis of diseases. There is a continuous demand to develop rapid and sensitive methods for the specific detection of nucleic acids. Herein, we constructed a highly sensitive and rapid fluorescent biosensor for the detection of BRCA1 by coupling a 3D DNA walker machine with spontaneous entropy-driven strand displacement reactions (ESDRs). In this study, the 3D DNA walker machine was well activated by the target DNA; this resulted in the cyclic utilization of the target DNA and the release of intermediate DNAs. Subsequently, the free intermediate DNAs triggered the circulation process of ESDRs with the help of the assistant probe A, leading to a significant enhancement of the fluorescence intensity. Due to the robust execution of the 3D DNA walker machine and highly efficient amplification capability of ESDRs, the developed biosensing method shows a wide linear range from 0.1 pM to 10 nM with the detection limit as low as 41.44 fM (S/N = 3). Moreover, the constructed biosensor displays superior specificity and has been applied to monitor BRCA1 in complex matrices. Thus, this elaborated cascade amplification biosensing strategy provides a potential platform for the bioassays of nucleic acids and the clinical diagnosis of diseases.

Nucleic acid analysis plays an important role in the diagnosis of diseases.

Recent advances in DNA nanotechnology

DNA is a powerful guiding molecule to achieve the precise construction of arbitrary structures and high-resolution organization of functional materials. The combination of sequence programmability, rigidity and highly specific molecular recognition in this molecule has resulted in a wide range of exquisitely designed DNA frameworks. To date, the impressive potential of DNA nanomaterials has been demonstrated from fundamental research to technological advancements in materials science and biomedicine. This review presents a summary of some of the most recent developments in structural DNA nanotechnology regarding new assembly approaches and efforts in translating DNA nanomaterials into practical use. Recent work on incorporating blunt-end stacking and hydrophobic interactions as orthogonal instruction rules in DNA assembly, and several emerging applications of DNA nanomaterials will also be highlighted.