Design of DNA nanostructure-based interfacial probes for the electrochemical detection of nucleic acids directly in whole blood

Ultra-sensitive detection of microRNAs using an electrochemical biosensor based on a PNA-DNA2 three-way junction nanostructure and dual cascade isothermal amplification

BACKGROUND

MiRNA expression profiles may serve as valuable biomarkers for early cancer diagnosis. However, the detection of miRNA remains greatly challenging due to its shorter length and lower abundance in cells. Electrochemical biosensors based on DNA nanostructures have attracted significant attention due to their improved capture efficiency, high sensitivity, and ease of miniaturization, but the complex construction process, non-specific interactions among DNA probes, and their low stability continue to severely restrict their widespread application in clinical diagnostics. Therefore, developing robust and sensitive methods for miRNA analysis is still of great value.

RESULTS

We describe an ultra-sensitive electrochemical biosensor for miRNA by integrating the PNA-DNA2 three-way junction (3WJ) nanostructure with target-recycling catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) dual cascade isothermal amplification. The target miRNA triggers CHA amplification, resulting in the generation of substantial quantities of double-stranded DNA (dsDNA) products. These dsDNA are subsequently captured by PNA probes immobilized on the electrode surface, leading to the formation of a densely packed layer of PNA-DNA2 3WJ nanostructure. Subsequently, the single-stranded termini of the two branches extending from 3WJ function as promoters to initiate the HCR, resulting in the formation of a layer of intricately intertwined branched long dsDNA molecules, which could adsorb substantial quantities of [Ru(NH3)6]3+, thereby significantly amplifying the electrochemical signal. This electrochemical biosensor exhibits exceptional sensitivity towards miRNA-21, achieving a detection limit as low as 2.9 aM while effectively discriminating single base mutations.

SIGNIFICANCE

This represents the first electrochemical system for miRNA detection by integrating the PNA-DNA2 3WJ with CHA-HCR dual cascade isothermal amplification. The robust, specific and ultrasensitive feature makes cancer cell miRNA monitoring possible, suggesting its great application prospect as a promising sensing platform for monitoring various miRNA biomarkers in cancer diagnostics.

Modular DNA origami-based electrochemical detection of DNA and proteins

The diversity and heterogeneity of biomarkers has made the development of general methods for single-step quantification of analytes difficult. For individual biomarkers, electrochemical methods that detect a conformational change in an affinity binder upon analyte binding have shown promise. However, because the conformational change must operate within a nanometer-scale working distance, an entirely new sensor, with a unique conformational change, must be developed for each analyte. Here, we demonstrate a modular electrochemical biosensor, built from DNA origami, which is easily adapted to diverse molecules by merely replacing its analyte binding domains. Instead of relying on a unique nanometer-scale movement of a single redox reporter, all sensor variants rely on the same 100-nm scale conformational change, which brings dozens of reporters close enough to a gold electrode surface that a signal can be measured via square-wave voltammetry, a standard electrochemical technique. To validate our sensor's mechanism, we used single-stranded DNA as an analyte, and optimized the number of redox reporters and various linker lengths. Adaptation of the sensor to streptavidin and Platelet-Derived Growth Factor-BB (PDGF-BB) analytes was achieved by simply adding biotin or anti-PDGF aptamers to appropriate DNA linkers. Geometrically optimized streptavidin sensors exhibited signal gain and limit of detection markedly better than comparable reagentless electrochemical sensors. After use, the same sensors could be regenerated under mild conditions: Performance was largely maintained over four cycles of DNA strand displacement and rehybridization. By leveraging the modularity of DNA nanostructures, our work provides a straightforward route to the single-step quantification of arbitrary nucleic acids and proteins.

DNA Tetrahedra as Functional Nanostructures: From Basic Principles to Applications

Self-assembled supramolecular DNA tetrahedra composed of programmed sequence-engineered complementary base-paired strands represent elusive nanostructures having key contributions to the development and diverse applications of DNA nanotechnology. By appropriate engineering of the strands, DNA tetrahedra of tuneable sizes and chemical functionalities were designed. Programmed functionalities for diverse applications were integrated into tetrahedra structures including sequence-specific recognition strands (aptamers), catalytic DNAzymes, nanoparticles, proteins, or fluorophore. The article presents a comprehensive review addressing methods to assemble and characterize the DNA tetrahedra nanostructures, and diverse applications of DNA tetrahedra framework are discussed. Topics being addressed include the application of structurally functionalized DNA tetrahedra nanostructure for the assembly of diverse optical or electrochemical sensing platforms and functionalized intracellular sensing and imaging modules. In addition, the triggered reconfiguration of DNA tetrahedra nanostructures and dynamic networks and circuits emulating biological transformations are introduced. Moreover, the functionalization of DNA tetrahedra frameworks with nanoparticles provides building units for the assembly of optical devices and for the programmed crystallization of nanoparticle superlattices. Finally, diverse applications of DNA tetrahedra in the field of nanomedicine are addressed. These include the DNA tetrahedra-assisted permeation of nanocarriers into cells for imaging, controlled drug release, active chemodynamic/photodynamic treatment of target tissues, and regenerative medicine.

Development of a Novel System Consisting of a Reductase-Like Nanozyme and the Reaction of Resazurin and Ammonia Borane for Sensitive Fluorometric Sensing

We report a novel system consisting of a redox reaction and a highly efficient reductase-like nanozyme, silica-palladium nanoparticles (Pd@SiO2 NPs), as a novel detection platform for fluorometric sensing. In a proof-of-concept demonstration using an oligonucleotide as the detection target, a glass fiber-based sensor is fabricated by covalently conjugating two oligo probes, which are complementary to the adjacent segments of the target oligonucleotide, on Pd@SiO2 NPs and glass fiber, respectively. In the presence of the target oligonucleotide, the two probes are drawn together by the target through sequence-specific hybridization, bringing the Pd@SiO2 NPs to the glass fiber. When the glass fiber is subsequently immersed in a mixture of resazurin and ammonia borane solution, the Pd@SiO2 NPs on the glass fiber trigger the catalytic conversion of resazurin (blue, slightly fluorescent) to resorufin (pink, highly fluorescent) with massive signal amplification, indirectly signaling the presence of the target oligonucleotide. We show that the glass fiber-based fluorometric sensor can detect a target oligonucleotide associated with the BRAF mutation linearly in the concentration range of 20 to 400 pM with a detection limit (LOD) of 15 pM and the specificity to differentiate targets with single-base difference. These results demonstrate a new frontier for the development of a sensitive, specific, and inexpensive nonenzyme-based fluorometric sensing platform as an alternative to conventional enzyme-based assays.

A Redox-Reversible Switch of DNA Hydrogen Bonding and Structure

Modulating molecular structure and function at the nanoscale drives innovation across wide-ranging technologies. Electrical control of the bonding of individual DNA base pairs endows DNA with precise nanoscale structural reconfigurability, benefiting efforts in DNA origami and actuation. Here, alloxazine DNA base surrogates were synthesized and incorporated into DNA duplexes to function as a redox-active switch of hydrogen bonding. Circular dichroism (CD) revealed that 24-mer DNA duplexes containing one or two alloxazines exhibited CD spectra and melting transitions similar to DNA with only canonical bases, indicating that the constructs adopt a B-form conformation. However, duplexes were not formed when four or more alloxazines were incorporated into a 24-mer strand. Thiolated duplexes incorporating alloxazines were self-assembled onto multiplexed gold electrodes and probed electrochemically. Square-wave voltammetry (SWV) revealed a substantial reduction peak centered at -0.272 V vs Ag/AgCl reference. Alternating between alloxazine oxidizing and reducing conditions modulated the SWV peak in a manner consistent with the formation and loss of hydrogen bonding, which disrupts the base pair stacking and redox efficiency of the DNA construct. These alternating signals support the assertion that alloxazine can function as a redox-active switch of hydrogen bonding, useful in controlling DNA and bioinspired assemblies.

Self-assembled methodologies for the construction of DNA nanostructures and biological applications

Over the past decades, deoxyribonucleic acid (DNA), as a versatile building block, has been widely employed to construct functionalized nanostructures. Among the diverse types of materials, DNA related nanostructures have gained growing attention due to their intrinsic programmability, favorable biocompatibility, and strong molecular recognition capability. The conventional construction strategy for building DNA structures is based on Watson-Crick base-pairing rules, which are mainly driven by the hydrogen bonding of bases. However, hydrogen bonding-based DNA nanostructures cannot meet the requirements of specific morphology and multifunctionality. Currently, various functional elements have been introduced to expand the synthetic methodologies for constructing the DNA hybrid nanostructures, including small molecules, peptide polymers, organic ligands and transition metal ions. Besides, the potential applications for these DNA hybrid nanostructures have also been explored. It has been demonstrated that DNA hybrid structures with various properties can be extensively applied in the fields of magnetic resonance, luminescence imaging, biomedical detection, and drug delivery systems. In this review, we highlight the pioneering contributions to the methodologies of DNA-based nanostructure assembly. Furthermore, the recent advances in drug delivery systems and biomedical diagnosis based on DNA hybrid nanostructures are briefly summarized.

Recent advances in the applications of DNA frameworks in liquid biopsy: A review

Cancer is one of the serious threats to public life and health. Early diagnosis, real-time monitoring, and individualized treatment are the keys to improve the survival rate and prolong the survival time of cancer patients. Liquid biopsy is a potential technique for cancer early diagnosis due to its non-invasive and continuous monitoring properties. However, most current liquid biopsy techniques lack the ability to detect cancers at the early stage. Therefore, effective detection of a variety of cancers is expected through the combination of various techniques. Recently, DNA frameworks with tailorable functionality and precise addressability have attracted wide spread attention in biomedical applications, especially in detecting cancer biomarkers such as circulating tumor cells (CTCs), exosomes and circulating tumor nucleic acid (ctNA). Encouragingly, DNA frameworks perform outstanding in detecting these cancer markers, but also face some challenges and opportunities. In this review, we first briefly introduced the development of DNA frameworks and its typical structural characteristics and advantages. Then, we mainly focus on the recent progress of DNA frameworks in detecting commonly used cancer markers in liquid-biopsy. We summarize the advantages and applications of DNA frameworks for detecting CTCs, exosomes and ctNA. Furthermore, we provide an outlook on the possible opportunities and challenges for exploiting the structural advantages of DNA frameworks in the field of cancer diagnosis. Finally, we envision the marriage of DNA frameworks with other emerging materials and technologies to develop the next generation of disease diagnostic biosensors.

Chronoamperometric interrogation of an electrochemical aptamer-based sensor with tetrahedral DNA nanostructure pendulums for continuous biomarker measurements

Tetrahedral DNA nanostructure (TDN) is highly promising in developing electrochemical aptamer-based (E-AB) sensors for biomolecular detection, owing to its inherit programmability, spatial orientation and structural robustness. However, current interrogation strategies applied for TDN-based E-AB sensors, including enzyme-based amperometry, voltammetry, and electrochemical impedance spectroscopy, either require complicated probe design or suffer from limited applicability or selectivity. In this study, a TDN pendulum-empowered E-AB sensor interrogated by chronoamperometry for reagent-free and continuous monitoring of a blood clotting enzyme, thrombin, was developed. TDN pendulums with extended aptamer sequences at three vertices were immobilized on a gold electrode via a thiolated double-stranded DNA (dsDNA) at the fourth vertex, and their motion is modulated by the bonding of target thrombin to aptamers. We observed a significantly amplified signalling output on our sensor based on the TDN pendulum compared to E-AB sensors modified with linear pendulums. Moreover, our sensor achieved highly selective and rapidly responsive measurement of thrombin in both PBS and artificial urine, with a wide dynamic range from 1 pM to 10 nM. This study shows chronoamperometry-enabled continuous biomarker monitoring on a sub-second timescale with a drift-free baseline, demonstrating a novel approach to accurately detect molecular dynamics in real time.

Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering

DNA monolayers with inherent chirality play a pivotal role across various domains including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), often lack structural orderliness and design flexibility at the interface. Structural DNA nanotechnology has emerged as a promising solution to tackle these challenges. In this study, we present a strategy for crafting highly adaptable twisted DNA origami-based chiral monolayers. These structures exhibit distinct interfacial assembly characteristics and effectively mitigate the structural disorder of dsDNA monolayers, which is constrained by a limited persistence length of ∼50 nm of dsDNA. We highlight the spin-filtering capabilities of seven representative DNA origami-based chiral monolayers, demonstrating a maximal one-order-of-magnitude increase in spin-filtering efficiency per unit area compared with conventional dsDNA chiral monolayers. Intriguingly, our findings reveal that the higher-order tertiary chiral structure of twisted DNA origami further enhances the spin-filtering efficiency. This work paves the way for the rational design of DNA chiral monolayers.

Proximity-Driven DNA Nanosensors

In proximity-driven sensing, interactions between a probe and an analyte produce a detectable signal by causing a change in distance of two probe components or signaling moieties. By interfacing such systems with DNA-based nanostructures, platforms that are highly sensitive, specific, and programmable can be designed. In this Perspective, we delineate the advantages of using DNA building blocks in proximity-driven nanosensors and provide an overview of recent progress in the field, from sensors that rapidly detect pesticides in food to probes that identify rare cancer cells in blood. We also discuss current challenges and identify key areas that need further development.

Methylene-Blue-Encapsulated Metal-Organic-Framework-Based Electrochemical POCT Platform for Multiple Detection of Heavy Metal Ions in Milk

Considering the high risk of heavy metal ions (HMIs) transferring through the food chain and accumulating in milk, a flexible and facile point-of-care testing (POCT) platform is urgently needed for the accurate, sensitive, and highly selective on-site quantification of multiple HMIs in milk. In this work, a cost-effective disk with six screen-printed electrodes (SPEs) was designed for hand-held electrochemical detection. Metal organic frameworks (MOFs) were adopted to amplify and enhance the electrochemical signals of methylene blue (MB). Using differential pulse voltammetry (DPV) methods, low limits of detection for four HMIs (Cd2+, 0.039 ppb; Hg2+, 0.039 ppb; Pb2+, 0.073 ppb; and As3+, 0.022 ppb) were achieved within four minutes. Moreover, the quantitative POCT system was applied to milk samples. The advantages of low cost, ease of on-site implementation, fast response, and accuracy allow for the POCT platform to be used in practical monitoring applications for the quantitation of multiple HMIs in milk samples.

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

Biomolecular sensors for advanced physiological monitoring

Body-based biomolecular sensing systems, including wearable, implantable and consumable sensors allow comprehensive health-related monitoring. Glucose sensors have long dominated wearable bioanalysis applications owing to their robust continuous detection of glucose, which has not yet been achieved for other biomarkers. However, access to diverse biological fluids and the development of reagentless sensing approaches may enable the design of body-based sensing systems for various analytes. Importantly, enhancing the selectivity and sensitivity of biomolecular sensors is essential for biomarker detection in complex physiological conditions. In this Review, we discuss approaches for the signal amplification of biomolecular sensors, including techniques to overcome Debye and mass transport limitations, and selectivity improvement, such as the integration of artificial affinity recognition elements. We highlight reagentless sensing approaches that can enable sequential real-time measurements, for example, the implementation of thin-film transistors in wearable devices. In addition to sensor construction, careful consideration of physical, psychological and security concerns related to body-based sensor integration is required to ensure that the transition from the laboratory to the human body is as seamless as possible.

Employing a Redox Reporter-Modified Self-Assembly Monolayer in Electrochemical Aptamer-Based Sensors to Enable Calibration-Free Measurements

Electrochemical aptamer-based (E-AB) sensors suffer from sensor-to-sensor signal variations due to the variation in the total number of probes immobilized on the sensor surface, the effective working area, and the heterogeneity properties of the electrode surface, thus requiring a calibration step prior to each measurement. This is impractical, if not possible, for some cases, e.g., in a complex matrix including blood samples. In response, we propose a calibration-free approach to achieve the measurement of biorelevant small-molecule and protein analytes. Specifically, we employed one reporter labeled onto an aptamer (e.g., methylene blue) for redox signaling, and the other reporter (e.g., ferrocene) was modified onto a self-assembly monolayer as a reference signal. By taking the ratio of the two signals, we achieved a much improved baseline stability and sensor-to-sensor reproducibility, which allows the calibration-free measurement of the analysis of the respective targets, including doxorubicin, vancomycin, and thrombin in both simple buffer and even directly complex samples including serum and whole blood.

Affinity-based electrochemical sensors for biomolecular detection in whole blood

The detection and/or quantification of biomarkers in blood is important for the early detection, diagnosis, and treatment of a variety of diseases and medical conditions. Among the different types of sensors for detecting molecular biomarkers, such as proteins, nucleic acids, and small-molecule drugs, affinity-based electrochemical sensors offer the advantages of high analytical sensitivity and specificity, fast detection times, simple operation, and portability. However, biomolecular detection in whole blood is challenging due to its highly complex matrix, necessitating sample purification (i.e., centrifugation), which involves the use of bulky, expensive equipment and tedious sample-handling procedures. To address these challenges, various strategies have been employed, such as purifying the blood sample directly on the sensor, employing micro-/nanoparticles to enhance the detection signal, and coating the electrode surface with blocking agents to reduce nonspecific binding, to improve the analytical performance of affinity-based electrochemical sensors without requiring sample pre-processing steps or laboratory equipment. In this article, we present an overview of affinity-based electrochemical sensor technologies that employ these strategies for biomolecular detection in whole blood.

Functional Xeno Nucleic Acids for Biomedical Application

Functional nucleic acids(FNAs) refer to a type of oligonucleotides with functions over the traditional genetic roles of nucleic acids, which have been widely applied in screening, sensing and imaging fields. However, the potential application of FNAs in biomedical field is still restricted by the unsatisfactory stability, biocompatibility, biodistribution and immunity of natural nucleic acids(DNA/RNA). Xeno nucleic acids(XNAs) are a kind of nucleic acid analogues with chemically modified sugar groups that possess improved biological properties, including improved biological stability, increased binding affinity, reduced immune responses, and enhanced cell penetration or tissue specificity. In the last two decades, scientists have made great progress in the research of functional xeno nucleic acids, which makes it an emerging attractive biomedical application material. In this review, we summarized the design of functional xeno nucleic acids and their applications in the biomedical field.

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.

Bioinspired superwettable electrodes towards electrochemical biosensing

Superwettable materials have attracted much attention due to their fascinating properties and great promise in several fields. Recently, superwettable materials have injected new vitality into electrochemical biosensors. Superwettable electrodes exhibit unique advantages, including large electrochemical active areas, electrochemical dynamics acceleration, and optimized management of mass transfer. In this review, the electrochemical reaction process at electrode/electrolyte interfaces and some fundamental understanding of superwettable materials are discussed. Then progress in different electrodes has been summarized, including superhydrophilic, superhydrophobic, superaerophilic, superaerophobic, and superwettable micropatterned electrodes, electrodes with switchable wettabilities, and electrodes with Janus wettabilities. Moreover, we also discussed the development of superwettable materials for wearable electrochemical sensors. Finally, our perspective for future research is presented.

Interfacial DNA Framework-Enhanced Background-to-Signal Transition for Ultrasensitive and Specific Micro-RNA Detection

Interfacial DNA self-assembly is fundamental to solid nucleic acid biosensors, whereas how to improve the signal-to-noise ratio has always been a challenge, especially in the charge-based electrochemical DNA sensors because of the large noise from the negatively charged DNA capture probes. Here, we report a DNA framework-reversed signal-gain strategy through background-to-signal transition for ultrasensitive and highly specific electrical detection of microRNAs (miRNAs) in blood. By using a model of enzyme-catalyzed deposition of conductive molecules (polyaniline) targeting to DNA, we observed the highest signal contribution per unit area by the highly charged three-dimensional (3D) tetrahedral DNA framework probe, relative to the modest of two-dimensional (2D) polyA probe and the lowest of one-dimensional (1D) single-stranded (ss)DNA probe, suggesting the positive correlation of background DNA charge with signal enhancement. Using such an effective signal-transition design, the DNA framework-based electrochemical sensor achieves ultrasensitive miRNAs detection with sensitivity up to 0.29 fM (at least 10-fold higher than that with 1D ssDNA or 2D polyA probes) and high specificity with single-base resolution. More importantly, this high-performance sensor allows for a generalized sandwich detection of tumor-associated miRNAs in the complex matrices (multiple cell lysates and blood serum) and further distinguishes the tumor patients (e.g., breast, lung, and liver cancer) from the normal individuals. These advantages signify the promise of this miRNA sensor as a versatile tool in precision diagnosis.

Functionalization of Covalent Organic Frameworks with DNA via Covalent Modification and the Application to Exosomes Detection

The functionalization of covalent organic frameworks (COFs) with biomacromolecules can extend their functions, which is the premise of their application in biomedical research. However, strategies to functionalize COFs with biomacromolecules, which can ensure the stability in complex medium and minimize the undesired effects, are still lacking. In this work, we have proposed a strategy to functionalize COFs with DNA by covalently linking DNA to the functional group on the COF surface through Cu(I)-catalyzed azide/alkyne cycloaddition (CuAAC) reaction. The as-prepared DNA-functionalized COFs (DNA-COFs) can exhibit good hybridization ability and cargo loading ability; thus, we have designed a DNA-COF-based nanoprobe and then fabricated an electrochemical biosensor for the detection of exosomes. In this design, the functionalization with DNA enables COFs to recognize and capture exosomes, and the encapsulation of a large number of methylene blue (MB) in COFs facilitates signal amplification, which can enhance the sensitivity of the biosensor. Moreover, by simply replacing the oligonucleotide sequences, the strategy proposed here can generally be used to build different DNA-COFs with diverse functions for broader biomedical applications.

Construction of a Degradation-Free DNA Conjugated Nanoprobe and Its Application in Rapid Field Screening for Sulfur Mustard

Sulfur mustard (SM) is a notorious blistering chemical warfare agent. Rapid field screening for trace SM is of vital significance for the detection of antiterrorism and timely treatment. Here, a visual assay for SM was constructed on the basis of its inhibition for the G-quadruplexes/hemin DNAzyme. Specifically, multiple guanine (G)-rich single stranded oligonucleotides (ssODN) named S1 (80% of G in the total bases), i.e., the precursor for G-quadruplex, which could oxide tetramethylbenzidine (TMB) to its green product, were conjugated on the nonfouling polymer brush grafted magnetic beads (MB@P(C-H)). SM could specifically alkylate the N7 and O6 sites of G in the S1; thus, it failed to form the DNAzyme based signal reporter. It was demonstrated that the nonfouling P(C-H) interface on the magnetic bead (MB) could protect the conjugated ssODN from nuclease degradation, thus ensuring its well sensing performance in complex samples. Under the optimized conditions, this method achieved good sensitivity and selectivity with a limit of detection (LOD) as low as 0.26 μmol L^-1, and the recoveries ranging from 86% to 117% were obtained for different SM spiked real samples. Above all, this method combining low cost and ready operation could be suited for rapid field SM screening in a wide range of environmental matrices.

Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers

Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.

Nucleic acid-based electrochemical biosensor: Recent advances in probe immobilization and signal amplification strategies

With the increasing importance of accurate and early disease diagnosis and the development of personalized medicine, DNA-based electrochemical biosensor has attracted broad scientific and clinical interests in the past decades due to its unique hybridization specificity, fast response time, and potential for miniaturization. In order to achieve high detection sensitivity, the design of DNA electrochemical biosensors depends critically on the improvement of the accessibility of target molecules and the enhancement of signal readout. Here, we summarize the recent advances in DNA probe immobilization and signal amplification strategies with a special focus on DNA nanostructure-supported DNA probe immobilization method, which provides the opportunity to rationally control the distance between probes and keep them in upright confirmation, as well as the contribution of functional nanomaterials in enhancing the signal amplification. The next challenge of biosensors will be the fabrication of point-of-care devices for clinical testing. The advancement of multidisciplinary areas, including nanofabrication, material science, and biochemistry, has exhibited profound promise in achieving such portable sensing devices. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.

Insight into the Influence of Analyte Molecular Structure Targeted on MoS2-GO-Coated Electrochemical Nanosensors

MoS₂-GO composites were fabricated by an ultrasonication method at room temperature. Raman spectra, emission scanning electron microscopy (SEM), and transmission electron microscopy (TEM) images were used to study the structural characteristics, morphologies, and sizes of the synthesized materials. An MoS₂-GO/SPE (screen-printed electrode) was prepared by a facile dropping method and acted as an effective electrochemical sensor toward clenbuterol (CLB) and 4-nitrophenol (4-NP) detection. Based on the obtained results, the influence of analyte molecular structure on the adsorption ability and electronic interoperability between the targeted analyte and electrode surface were investigated in detail and discussed as well, through some electrochemical kinetic parameters (electron/proton-transfer number, electron transfer rate constant (k_s), charge transfer coefficient, and adsorption capacity (Γ)). In particular, it should be stressed that 4-NP molecules possess a simple molecular structure with many positive effects (electronic, conjugation, and small steric effects) and flexible functional groups, resulting in fast electron transport/charge diffusion and effective adsorption process as well as strong interactions with the electrode surface. Therefore, 4-NP molecules have been facilitated better in electrochemical reactions at the electrode surface and electrode-electrolyte interfaces, leading to improved current response and electrochemical sensing performance, compared with those of CLB.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

Radiolabeling and Preliminary Evaluation of 99mTc-Labeled DNA Cube Nanoparticles as Potential Tracers for SPECT Imaging

Purpose

DNA nanostructures, with the advantages of structural designability and spatial addressability, have shown a great potential in the field of drug delivery and bio-medicine. Herein, we aimed to prepare technetium-99m radiolabeled DNA cube nanoparticles (^99mTc-DCN) and expect to build a DCN-based drug carrier and nuclear medicine imaging platform.

Methods

DCN could be readily assembled with 6 designed DNA oligonucleotides at an equal mole ratio in a single annealing procedure. ^99mTc-MAG3-ssDNA (A20) was obtained by labeling MAG3-ssDNA (A20) with technetium-99m by using a stannous chloride reduction method. ^99mTc-DCN was prepared by hybridize DCN with side chains (T20-DCN) with ^99mTc-MAG3-ssDNA (A20). The biodistribution study and SPECT/CT imaging were conducted on KM mice.

Results

DCN was successfully assembled, and as-prepared DCN was characterized by native polyacrylamide gel electrophoresis, atomic force microscope and fluorescence resonance energy transfer. The size of DCN was about 5 nm. The radiolabeling yield of ^99mTc-MAG3-ssDNA (A20) was approximately 90% by radio thin-layer chromatography. T20-DCN mixed with ^99mTc-MAG3-ssDNA (A20) in PBS could generate ^99mTc-DCN upon hybridization. The retention time (RT) of ^99mTc-MAG3-ssDNA (A20) was at ~22 min, and the RT of as-prepared ^99mTc-DCN was at ~12 min by radio-HPLC. The results from biodistribution study and SPECT/CT imaging showed that a significant proportion of DCNs were metabolized through the liver and kidney. Intestine exhibited a relatively indicative signal as well, which might be explained by the enterohepatic circulation of DCN via the liver and gallbladder.

Conclusion

We have successfully prepared ^99mTc-DCN as a SPECT/CT imaging probe via the side-chain hybridization strategy. The probe was metabolized mainly by the liver and excreted primarily to the bladder. Due to the superior properties of DNA cube nanoparticles, we believe DCN may potentially be translated into a preclinical setting for diagnosis and treatment of cancer-related diseases.

Engineering a Rolling-Circle Strand Displacement Amplification Mediated Label-Free Ultrasensitive Electrochemical Biosensing Platform

In this work, an original rolling-circle strand displacement amplification (RC-SDA) was developed by introducing a circle DNA with two recognition domains as a template instead of the limited liner DNA template in traditional strand displacement amplification (SDA), which displayed much shorter reaction time down to 30 min and quite higher conversion efficiency of more than 1.77 × 10⁸ compared with those of traditional strand displacement amplification (SDA) and could be applied to construct a label-free biosensor for ultrasensitive detection of an HIV DNA fragment. Once the target HIV DNA fragment interacts with the template circle DNA, the RC-SDA could be activated to dramatically output amounts of mimic target DNA with the assistance of the Phi29 DNA polymerase and Nb.BbvCI enzyme. In application, while the output products were captured by the DNA tetrahedral nanoprobe (DTNP) modified electrode, the electrochemical tag silver nanoclusters (AgNCs) on DTNP would be released from the electrode surface, accompanied with an obviously decreased electrochemical signal. This way, the developed signal-off biosensor was successfully applied to realize the rapid and ultrasensitive detection of target HIV DNA fragment with a detection limit down to 0.21 fM, which exploits the new generation of a universal strategy beyond the traditional ones for applications in biosensing assay, clinic diagnosis, and DNA nanobiotechnology.

Strategies for Biomolecular Analysis and Continuous Physiological Monitoring

Portable devices capable of rapid disease detection and health monitoring are crucial to decentralizing diagnostics from clinical laboratories to the patient point-of-need. Although technologies have been developed targeting this challenge, many require the use of reporter molecules or reagents that complicate the automation and autonomy of sensors. New work in the field has targeted reagentless approaches to enable breakthroughs that will allow personalized monitoring of a wide range of biomarkers on demand. This Perspective focuses on the ability of reagentless platforms to revolutionize the field of sensing by allowing rapid and real-time analysis in resource-poor settings. First, we will highlight advantages of reagentless sensing techniques, specifically electrochemical detection strategies. Advances in this field, including the development of wearable and in situ sensors capable of real-time monitoring of biomarkers such as nucleic acids, proteins, viral particles, bacteria, therapeutic agents, and metabolites, will be discussed. Reagentless platforms which allow for wash-free, calibration free-detection with increased dynamic range are highlighted as a key technological advance for autonomous sensing applications. Furthermore, we will highlight remaining challenges which must be overcome to enable widespread use of reagentless devices. Finally, future prospects and potential breakthroughs in precision medicine that will arise as a result of further development of reagentless sensing approaches are discussed.

Functionalized nanoprobes for in situ detection of telomerase

Telomerase, a special ribonucleoprotein reverse transcriptase, can maintain the length and stability of telomeres and plays an important role in cell proliferation and differentiation. Due to the distinguishable expression level in normal cells and cancer cells, telomerase has become an important biomarker for cancer diagnosis and prognosis evaluation. Despite major breakthroughs in the field of telomerase detection, the extracts in the cell lysate are still the first choice as the analyte nevertheless, which will bring serious inaccuracies compared with the real intracellular activity. With the development of nanotechnology and nanomaterials, extraordinary progress has been made in telomerase detection by employing different versatile nanoprobes. In this review, we list the superiority of nanoprobes and systematically summarize the applications of nanoprobes in telomerase detection from the aspects of various nanomaterials and discuss the current challenges and potential trends in the future design of nanoprobes.

DNA Transformations for Diagnosis and Therapy

Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.

Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices

Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. A variety of factors can influence conformation, including temperature, ionic strength, pH, buffer cation valency, strand length, and sequence. To better understand the effects of these factors on immobilized DNA structures, we employ temperature-controlled electrochemical microsensors to study the effects of salt concentration and temperature variation on the conformation and motion of polythymine (polyT) strands of varying lengths (10, 20, 50 nucleotides). PolyT strands were tethered to a gold working electrode at the proximal end through a thiol linker via covalent bonding between the Au electrode and sulfur link, which can tend to decompose between a temperature range of 60 and 90 °C. The strands were also modified with an electrochemically active methylene blue (MB) moiety at the distal end. Electron transfer (eT) was measured by square wave voltammetry (SWV) and used to infer information pertaining to the average distance between the MB and the working electrode. We observe changes in DNA flexibility due to varying ionic strength, while the effects of increased DNA thermal motion are tracked for elevated temperatures. This work elucidates the behavior of ssDNA in the presence of a phosphate-buffered saline at NaCl concentrations ranging from 20 to 1000 mmol/L through a temperature range of 10-50 °C in 1° increments, well below the decomposition temperature range. The results lay the groundwork for studies on more complex DNA strands in conjunction with different chemical and physical conditions.

Recent Advances in Electrochemical Sensors for the Detection of Biomolecules and Whole Cells

Electrochemical sensors are considered an auspicious tool to detect biomolecules (e.g., DNA, proteins, and lipids), which are valuable sources for the early diagnosis of diseases and disorders. Advances in electrochemical sensing platforms have enabled the development of a new type of biosensor, enabling label-free, non-destructive detection of viability, function, and the genetic signature of whole cells. Numerous studies have attempted to enhance both the sensitivity and selectivity of electrochemical sensors, which are the most critical parameters for assessing sensor performance. Various nanomaterials, including metal nanoparticles, carbon nanotubes, graphene and its derivatives, and metal oxide nanoparticles, have been used to improve the electrical conductivity and electrocatalytic properties of working electrodes, increasing sensor sensitivity. Further modifications have been implemented to advance sensor platform selectivity and biocompatibility using biomaterials such as antibodies, aptamers, extracellular matrix (ECM) proteins, and peptide composites. This paper summarizes recent electrochemical sensors designed to detect target biomolecules and animal cells (cancer cells and stem cells). We hope that this review will inspire researchers to increase their efforts to accelerate biosensor progress-enabling a prosperous future in regenerative medicine and the biomedical industry.

Electrochemical DNA Sensors Based on MoS2-AuNPs for Polynucleotide Kinase Activity and Inhibition Assay

The determination of T4 polynucleotide kinase (PNK) activity and the screening of PNK inhibitors are critical to disease diagnosis and drug discovery. Numerous electrochemical strategies have been developed for the sensitive measurement of PNK activity and inhibition. However, they often suffer from additional labels and multiple steps of the detection process for the electrochemical readout. Herein, we have demonstrated an electrochemical DNA (E-DNA) sensor for the one-step detection of PNK with "signal-on" readout with no need for additional labels. In our design, the highly switchable double-stranded DNA (dsDNA) probes are immobilized on the gold nanoparticle-decorated molybdenum disulfide nanomaterial (MoS₂-AuNPs), which possesses large surface area and high conductivity for elevating the signal gain in the PNK detection. This signal-on E-DNA sensor integrated with MoS₂-AuNPs exhibits a much higher sensitivity than that without MoS₂-AuNPs, showing a detection limit of 2.18 × 10^-4 U/mL. Furthermore, this assay shows high selectivity, with the ability to discriminate PNK from other enzymes and proteins, and can be utilized to screen inhibitors. The proposed sensor is easy to operate with one-step readout and robust for PNK detection in the biological matrix and shows great potential for point-of-care in clinical diagnostics and drug screening.

High-Fidelity Determination and Tracing of Small Extracellular Vesicle Cargoes

Direct tracing of small extracellular vesicle (sEV) cargoes holds unprecedented importance for elucidating the mechanisms involved in intercellular communication. However, high-fidelity determination of sEVs' molecular cargoes in situ has yet to be achieved due to the difficulty in transporting molecular probes into intact sEVs. Herein, a fLuorescent Intracellular-Guided Hairpin-Tetrahedron (fLIGHT) nanoprobe is described for direct visualization of sEV microRNAs in situ. Integrating the advantages of nondestructive sEV penetration via DNA origami and single-nucleotide discrimination as well as wash-free fluorescence readout using a hairpin probe, the proposed approach enables high-fidelity fluorescence visualization of sEVs' microRNA without RNA extraction or leakage, demonstrating the potential of on-site tracing of sEV cargoes. This strategy opens an avenue to establishing universal molecular detection and labeling platforms that can facilitate both sEV-derived fundamental biological studies and molecular diagnostics.

Bio-inspired construction of a semi-artificial enzyme complex for detecting histone acetyltransferases activity

Herein, an electrochemical method to detect histone acetyltransferases activity (HAT) has been developed based on the reduction of G-Quadruplex-Cu(ii) metalloenzyme activity. A G-quadruplex-Cu(ii) metalloenzyme has excellent peroxidase property, generating strong electrochemical signal. In the presence of HAT, it can catalyze substrate peptide acetylation and produce large amounts of Coenzyme A (CoA). The electrochemical signal of G-Quadruplex-Cu(ii) is weak due to the competitive combination between G-Quadruplex and CoA with Cu(ii), resulting in the direct quantitative detection of HAT. The detection limit for HAT is about 0.14 nM using this strategy and the cost is quite low since the developed assay method is label-free and antibody-free due to the use of low-cost DNA and Cu2+. Since this assay method can be employed to detect HAT in serum, it may be useful in disease diagnosis in the future.

Grafting homogenous electrochemical biosensing strategy based on reverse proximity ligation and Exo III assisted target circulation for multiplexed communicable disease DNA assay

Rapid and effective diagnosis of communicable disease is one of the critical issues of the modern society, especially for detecting different targets at the same time. In this work, a grafting homogenous electrochemical biosensing strategy is proposed by integrating of reverse proximity ligation and exonuclease III (Exo III) assisted target circulation to analyze hepatitis B (HBV) and human immunodeficiency (HIV). Specially, a two-wing nanodevice (TWD) with two detection paths is elaborately designed based on analogous proximity ligation assay. The reverse proximity ligation process provides a new way of signal conversion and amplification, what accomplished by demolishing the TWD in the presence of targets. Meanwhile, a vast number of signal probes are released via Exo III assisted target circulation. Then the signal probes are grafted on the universal sensing interface, which is decorated with graftable tetrahedron DNA (GTD). These lead to a highly amplified electrochemical signal. Compared with the conventional strategies, the grafting homogenous electrochemical biosensing strategy not only achieves convenient sensitive detection of multiple communicable diseases DNA simultaneously, but also performs well in the detection of sole target. This strategy effectively decreases the background, homogenizes the distribution of probes, and avoids the complex and time-consuming modification process of the working electrode, which holds great potential application in early diagnosis for communicable disease in the future.

Dynamic DNA Assemblies in Biomedical Applications

Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.

Beyond Sensitive and Selective Electrochemical Biosensors: Towards Continuous, Real-Time, Antibiofouling and Calibration-Free Devices

Nowadays, electrochemical biosensors are reliable analytical tools to determine a broad range of molecular analytes because of their simplicity, affordable cost, and compatibility with multiplexed and point-of-care strategies. There is an increasing demand to improve their sensitivity and selectivity, but also to provide electrochemical biosensors with important attributes such as near real-time and continuous monitoring in complex or denaturing media, or in vivo with minimal intervention to make them even more attractive and suitable for getting into the real world. Modification of biosensors surfaces with antibiofouling reagents, smart coupling with nanomaterials, and the advances experienced by folded-based biosensors have endowed bioelectroanalytical platforms with one or more of such attributes. With this background in mind, this review aims to give an updated and general overview of these technologies as well as to discuss the remarkable achievements arising from the development of electrochemical biosensors free of reagents, washing, or calibration steps, and/or with antifouling properties and the ability to perform continuous, real-time, and even in vivo operation in nearly autonomous way. The challenges to be faced and the next features that these devices may offer to continue impacting in fields closely related with essential aspects of people's safety and health are also commented upon.

Highly sensitive detection of multiple antibiotics based on DNA tetrahedron nanostructure-functionalized magnetic beads

Functional DNAs-functionalized magnetic beads (MBs) offer great potential in bioanalysis field because of their target recognition and magnetic separation functions. However, the recognition capability and hybridization affinity of DNA probes often suffer from limited available space, poor probe conformation and non-selective adsorption. To overcome these limitations, we herein used aptamer-pendant DNA tetrahedron nanostructure-functionalized MBs (TETapt-tet MBs) to develop a target-response fluorescence method with tetracycline (TET) as a model. In the absence of TET, 6-carboxy-X-rhodamine-labeled complementary DNAs (ROX-cDNAs) were assembled on the surface of MBs. Upon the addition of target TET, the ROX-cDNAs were separated and released from the MBs to generate fluorescence signal. The limit of detection and limit of quantification for TET were found to be 6 pg mL^-1 and 20 pg mL^-1, respectively. Compared with ssDNA-functionalized MBs surface, the designed DNA tetrahedron nanostructure-based surface could decrease the hybridization time and reduce false positives, ensuring the accuracy of TET detection in complex samples. The presented method was successfully employed for TET detection in honey samples. Moreover, this functionalization strategy could be extended to detect multiple antibiotics by simply substituting different aptamer sequences. Therefore, the proposed method has great potential in the field of food safety and public health.

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 Electrochemical Biosensor Designed by Using Zr-Based Metal-Organic Frameworks for the Detection of Glioblastoma-Derived Exosomes with Practical Application

Glioblastoma (GBM) is one of the most fatal tumors in the brain, and its early diagnosis remains technically challenging due to the complex repertoires of oncogenic alterations and blood-brain barrier (BBB). GBM-derived specific exosomes can cross the BBB and circulate in body fluids, so they can be noninvasive biomarkers for the early diagnosis of GBM. Herein, we propose a sensitive and label-free electrochemical biosensor designed by using Zr-based metal-organic frameworks (Zr-MOFs) for the detection of GBM-derived exosomes with practical application. In the design, a peptide ligand can specifically bind with human epidermal growth factor receptor (EGFR) and EGFR variant (v) III mutation (EGFRvIII), which are overexpressed on the GBM-derived exosomes. Meanwhile, Zr-MOFs encapsulated with methylene blue can absorb on the surface of the exosomes due to the interaction between Zr⁴⁺ and the intrinsic phosphate groups outside of exosomes. Consequently, the concentration of exosomes can be directly quantified by monitoring the electroactive molecules inside MOFs, ranging from 9.5 × 10³ to 1.9 × 10⁷ particles/μL with the detection of limit of 7.83 × 10³ particles/μL. Furthermore, this proposed biosensor can distinguish GBM patients from healthy groups, demonstrating the great prospect for early clinical diagnosis.

A tetrahedral DNA nanostructure-decorated electrochemical platform for simple and ultrasensitive EGFR genotyping of plasma ctDNA

In this study, we propose an on-site electrochemical platform for sensitive simultaneous genotyping of the two major EGFR mutations (19del and L858R) through plasma ctDNA based on tetrahedral DNA nanostructure decorated screen-printed electrodes.