DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development

Bifunctional Protein TC1 Mediated One-Pot Strategy for Robust Immobilization of DNA with High Accessibility

Immobilizing DNA with high accessibility at the interface is attractive but challenging. Current methods often involve multiple chemical reactions and derivatives. In this study, an endonuclease, TC1, is introduced to develop a robust strategy for immobilizing DNA with enhanced accessibility. TC1 enables direct immobilization of DNA onto a solid support through self-catalytic DNA covalent coupling and robust solid adsorption capabilities. This method demonstrates high accessibility to target molecules, supported by the improved sensitivity of DNA hybridization and aptamer-target recognition assays. TC1-mediated DNA immobilization is a one-pot reaction that does not require chemical derivatives, making it promising for the development of high-performance DNA materials and technologies.

A trivalent aptasensor by using DNA tetrahedron as scaffold for label-free determination of antibiotics

Owing to advantage in high sensitivity and fast response, aptamer based electrochemical biosensors have attracted much more attention. However, inappropriate interfacial engineering strategy leads to poor recognition performance, which ascribe to the following factors of immobilized oligonucleotide strand including steric hindrance, interchain entanglement, and unfavorable conformation. In this work, we proposed a DNA tetrahedron based diblock aptamer immobilized strategy for the construction of label-free electrochemical biosensor. The diblock aptamer sequence is composite of T-rich anchor domain and recognition domain, where T-rich domain enabling anchored on the edge of DNA tetrahedron via Hoogsteen hydrogen bond at neutral condition. The DNA tetrahedron scaffold offers an appropriate lateral space for target recognition of diblock aptamer. More importantly, this trivalent aptamer recognition interface can be regenerated by simply adjusting the pH environment to alkaline, resulting in the dissociation of diblock aptamer. Under the optimum condition, proposed electrochemical aptasensor manifested a satisfied sensitivity for aminoglycosides antibiotic, kanamycin with a limit of detection of 0.69 nM, which is 45-fold lower than traditional Au-S immobilization strategy. Moreover, the proposed aptasensor had also successfully been extended to ampicillin detection by changing the sequence of recognition domain in diblock aptamer. This work paves a new way for the rational design of aptamer-based electrochemical sensor.

Life at the interface: Engineering bio-nanomaterials through interfacial molecular self-assembly

Interfacial self-assembly describes the directed organization of molecules and colloids at phase boundaries. Believed to be fundamental to the inception of primordial life, interfacial assembly is exploited by a myriad of eukaryotic and prokaryotic organisms to execute physiologic activities and maintain homeostasis. Inspired by these natural systems, chemists, engineers, and materials scientists have sought to harness the thermodynamic equilibria at phase boundaries to create multi-dimensional, highly ordered, and functional nanomaterials. Recent advances in our understanding of the biophysical principles guiding molecular assembly at gas-solid, gas-liquid, solid-liquid, and liquid-liquid interphases have enhanced the rational design of functional bio-nanomaterials, particularly in the fields of biosensing, bioimaging and biotherapy. Continued development of non-canonical building blocks, paired with deeper mechanistic insights into interphase self-assembly, holds promise to yield next generation interfacial bio-nanomaterials with unique, and perhaps yet unrealized, properties. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies.

PET image-guided kidney injury theranostics enabled by a bipyramidal DNA framework

Understanding the pharmacokinetic profiles of nanomaterials in living organisms is essential for their application in disease treatment. Bipyramidal DNA frameworks (BDFs) are a type of DNA nanomaterial that have shown prospects in the fields of molecular imaging and therapy. To serve as a reference for disease-related studies involving the BDF, we constructed a 68Ga-BDF and employed positron emission tomography (PET) imaging to establish its pharmacokinetic model in healthy mice. Our investigation revealed that the BDF was primarily eliminated from the body via the urinary system. Ureteral obstruction could significantly alter the metabolism of the urinary system. By utilizing the established pharmacokinetic model, we sensitively observed distinct imaging indicators in unilateral ureteral obstruction and acute kidney injury (a complication of ureteral obstruction) mouse models. Furthermore, we observed that the BDF showed therapeutic effects in an AKI model. We believe that the established pharmacokinetic model and unique renal excretion characteristics of the BDF will provide researchers with more information for studying kidney diseases.

Functionalized tetrahedral DNA frameworks for the capture of circulating tumor cells

Identification and characterization of circulating tumor cells (CTCs) from blood samples of patients with cancer can help monitor parameters such as disease stage, disease progression and therapeutic efficiency. However, the sensitivity and specificity of current multivalent approaches used for CTC capture is limited by the lack of control over the ligands' position. In this Protocol Update, we describe DNA-tetrahedral frameworks anchored with aptamers that can be configured with user-defined spatial arrangements and stoichiometries. The modified tetrahedral DNA frameworks, termed 'n-simplexes', can be used as probes to specifically target receptor-ligand interactions on the cell membrane. Here, we describe the synthesis and use of n-simplexes that target the epithelial cell adhesion molecule expressed on the surface of CTCs. The characterization of the n-simplexes includes measuring the binding affinity to the membrane receptors as a result of the spatial arrangement and stoichiometry of the aptamers. We further detail the capture of CTCs from patient blood samples. The procedure for the preparation and characterization of n-simplexes requires 11.5 h, CTC capture from clinical samples and data processing requires ~5 h per six samples and the downstream analysis of captured cells typically requires 5.5 h. The protocol is suitable for users with basic expertise in molecular biology and handling of clinical samples.

Enzymatic Synthesis of TNA Protects DNA Nanostructures

Xeno-nucleic acids (XNAs) are synthetic genetic polymers with improved biological stabilities and offer powerful molecular tools such as aptamers and catalysts. However, XNA application has been hindered by a very limited repertoire of tool enzymes, particularly those that enable de novo XNA synthesis. Here we report that terminal deoxynucleotide transferase (TdT) catalyzes untemplated threose nucleic acid (TNA) synthesis at the 3' terminus of DNA oligonucleotide, resulting in DNA-TNA chimera resistant to exonuclease digestion. Moreover, TdT-catalyzed TNA extension supports one-pot batch preparation of biostable chimeric oligonucleotides, which can be used directly as staple strands during self-assembly of DNA origami nanostructures (DONs). Such TNA-protected DONs show enhanced biological stability in the presence of exonuclease I, DNase I and fetal bovine serum. This work not only expands the available enzyme toolbox for XNA synthesis and manipulation, but also provides a promising approach to fabricate DONs with improved stability under the physiological condition.

Topology- and size-dependent binding of DNA nanostructures to the DNase I

The susceptibility of DNA nanomaterials to enzymatic degradation in biological environments is a significant obstacle limiting their broad applications in biomedicine. While DNA nanostructures exhibit some resistance to nuclease degradation, the underlying mechanism of this resistance remains elusive. In this study, the interaction of tetrahedral DNA nanostructures (TDNs) and double-stranded DNA (dsDNA) with DNase I is investigated using all-atom molecular dynamics simulations. Our results indicate that DNase I can effectively bind to all dsDNA molecules, and certain key residues strongly interact with the nucleic bases of DNA. However, the binding of DNase I to TDNs exhibits a non-monotonic behavior based on size; TDN15 and TDN26 interact weakly with DNase I (∼ - 75 kcal/mol), whereas TDN21 forms a strong binding with DNase I (∼ - 110 kcal/mol). Furthermore, the topological properties of the DNA nanostructures are analyzed, and an under-twisting (∼32°) of the DNA helix is observed in TDN15 and TDN26. Importantly, this under-twisting results in an increased width of the minor groove in TDN15 and TDN26, which primarily explains their reduced binding affinity to DNase I comparing to the dsDNA. Overall, this study demonstrated a novel mechanism for local structural control of DNA at the nanoscale by adjusting the twisting induced by length.

Correlated Hybrid DNA Structures Explored by the oxDNA Model

Thermodynamically, perfect DNA hybridization can be formed between probes and their corresponding targets due to the favorable energy. However, this is not the case dynamically. Here, we use molecular dynamics (MD) simulations based on the oxDNA model to investigate the process of DNA microarray hybridization. In general, correlated hybrid DNA structures are formed, including one probe associated with several targets as well as one target hybrid with multiple probes leading to the target-mediated hybridization. The formation of these two types of correlated structures largely depends on the surface coverage of the DNA microarray. Moreover, DNA sequence, DNA length, and spacer length have an impact on the structural formation. Our findings shed light on the dynamics of DNA hybridization, which is important for the application of DNA microarray.

Application of DNA Nanotweezers in biosensing: Nanoarchitectonics and advanced challenges

Deoxyribonucleic acid (DNA) is a carrier of genetic information. DNA hybridization is characterized by predictability, diversity, and specificity owing to the strict complementary base-pairing assembly mode, which stimulates the use of DNA to build a variety of nanomachines, including DNA tweezers, motors, walkers, and robots. DNA nanomachines have become prevalent for signal amplification and transformation in the field of biosensing, providing a new method for constructing highly sensitive sensing analysis strategies. DNA tweezers have exhibited unique advantages in biosensing applications owing to their simple structures and fast responses. The two-state conformation of DNA tweezers, the open and closed states, enable them to open and close autonomously after stimulation, thus facilitating the quick detection of corresponding signal changes of different targets. This review discusses the recent progress in the application of DNA nanotweezers in the field of biosensing, and the trends in their development for application in the field of biosensing are summarized.

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.

Cation and buffer specific effects on the DNA-lipid interaction

Knowledge of DNA - lipid layer interactions is key for the development of biosensors, synthetic nanopores, scaffolds, and gene-delivery systems. These interactions are strongly affected by the ionic composition of the solvent. We have combined quartz crystal microbalance (QCM) and ellipsometry measurements to reveal how pH, buffers and alkali metal chloride salts affect the interaction of DNA with lipid bilayers (DOTAP/DOPC 30:70 in moles). We found that the thickness of the DNA layer adsorbed onto the lipid bilayer decreased in the order citrate > phosphate > Tris > HEPES. The effect of cations on the thickness of the DNA layer decreased in the order (K⁺ > Na⁺ > Cs⁺ ∼ Li⁺). Rationalization of the experimental results requires that adsorption, due to cation specific charge screening, is driven by the simultaneous action of two mechanisms namely, the law of matching water affinities for kosmotropes (Li⁺) and ion dispersion forces for chaotropes (Cs⁺). The outcome of these two opposing mechanisms is a ^"bell-shaped" specific cations sequence. Moreover, a superimposed buffer specificity, which goes beyond the simple effect of pH regulation, further modulated cation specificity. In summary, DNA-lipid bilayer interactions are maximized if citrate buffer (50 mM, pH 7.4) and KCl (100 mM) are used.

Simultaneous Imaging and Visualizing the Association of Survivin mRNA and Telomerase in Living Cells by Using a Dual-Color Encoded DNA Nanomachine

Simultaneous imaging and especially visualizing the association of survivin mRNA and telomerase in living cells are of great value for the diagnosis and prognosis of cancer because their co-expression facilitates the development of cancer and identifies patients at high risk of tumor-related death. The challenge is to develop methods that enable visualizing the association of multiplex targets and avoid the distorted signals due to the different delivery efficiency of probes. Herein, we engineered a DNA triangular prism nanomachine (DTPN) for simultaneous multicolor imaging of survivin mRNA and telomerase and visualizing their association in living cells. Two recognizing probes targeted survivin mRNA and telomerase, and the reporter probe was assembled on the DTP in equal amounts, ensuring the same delivery efficiency of the probes to the living cells. The results showed that this DTPN could quantify intracellular survivin mRNA expression and telomerase activity. Moreover, it also enabled us to visualize the effect of the down-regulation of one target on the expression of another target under different drug stimulations. The results implied that our DTPN provided a promising platform for cancer diagnosis, prognosis, drug screening, and related biological research.

Novel DNA nanoflower biosensing technologies towards next-generation molecular diagnostics

DNA nanoflowers (DNFs) are topological flower-like nanostructures based on ultralong-strand DNA and inorganic metal-ion frameworks. Because of their programmability, biocompatibility, and controllable assembly size for specific responses to molecular recognition stimuli, DNFs are powerful biosensing tools for detecting biomolecules. Here, we review the current state of DNF-based biosensing strategies for in vivo and in vitro detection, with a view of how the field has evolved towards molecular diagnostics. We also provide a detailed classification of DNF-based biosensing strategies and propose their future utility. Particularly as transduction elements, DNFs can accelerate biosensing engineering by signal amplification. Finally, we discuss the key challenges and further prospects of DNF-based biosensing technologies in developing applications of a broader scope.

Albumin-Coated Framework Nucleic Acids as Bionic Delivery System for Triple-Negative Breast Cancer Therapy

Triple-negative breast cancer (TNBC) is a subtype of breast cancer, and it has aggressive and more frequent tissue metastases than other breast cancer subtypes. Because the proliferation of TNBC tumor cells does not depend on estrogen receptor (ER), progesterone receptor (PR), and Erb-B2 receptor tyrosine kinase 2 (HER2) and lacks accurate drug targets, conventional chemotherapy is challenging to be effective, and adverse reactions are severe. At present, the treatment strategy for TNBC generally depends on a combination of surgery, radiotherapy, and chemotherapy. Conventional administration methods have minimal effects on TNBC and cause severe damage to normal tissues. Therefore, it is an urgent task to develop an efficient and practical way of drug delivery and open up a new horizon of targeted therapy for TNBC. In our work, bovine serum albumin (BSA) acted as the protective film to prolong the circulation time of the tetrahedral framework nucleic acid (tFNA) delivery system and resist immune clearance in vivo. tFNA was used as a carrier loaded with DOX and AS1411 aptamers for the targeted treatment of triple-negative breast cancer. Compared with existing approaches, this optimized system exhibits stronger tumor-targeting so that tFNAs can be more concentrated around the tumor tissue, reducing DOX toxicity to other organs. This bionic delivery system exhibited effective tumor growth inhibition in the TNBC mice model, offering the clinical potential to promote the treatment of TNBC with great potential for clinical translation.

Preparation, applications, and challenges of functional DNA nanomaterials

As a carrier of genetic information, DNA is a versatile module for fabricating nanostructures and nanodevices. Functional molecules could be integrated into DNA by precise base complementary pairing, greatly expanding the functions of DNA nanomaterials. These functions endow DNA nanomaterials with great potential in the application of biomedical field. In recent years, functional DNA nanomaterials have been rapidly investigated and perfected. There have been reviews that classified DNA nanomaterials from the perspective of functions, while this review primarily focuses on the preparation methods of functional DNA nanomaterials. This review comprehensively introduces the preparation methods of DNA nanomaterials with functions such as molecular recognition, nanozyme catalysis, drug delivery, and biomedical material templates. Then, the latest application progress of functional DNA nanomaterials is systematically reviewed. Finally, current challenges and future prospects for functional DNA nanomaterials are discussed.

Dissipative DNA nanotechnology

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature.

Activatable Dual Cancer-Related RNA Imaging and Combined Gene-Chemotherapy through the Target-Induced Intracellular Disassembly of Functionalized DNA Tetrahedron

The desire for a cancer theranostic system with simultaneously accurate diagnosis and efficient therapy is undeniably interminable. Heretofore, theranostic systems with simple components were designed for cancer theranostics but with confined accuracy of diagnosis and side effects of administered drugs. Here, we report an activatable theranostic system for simultaneously imaging dual cancer-related RNAs, mRNA Bcl-2 and piRNA-36026, and combined gene-chemotherapy through the target-induced intracellular disassembly of DNA tetrahedron. Briefly, five customized oligonucleotides are used to assemble the functionalized DNA tetrahedron. The relevant functional nucleic acids, including the antisequence of mRNA Bcl-2, the antisequence of piRNA-36026, and aptamer AS1411, are designed in the customized oligonucleotides with the signal reporters Cy3 and Cy5. Doxorubicin (DOX) is loaded in the functionalized DNA tetrahedron by inlaying between cytosine and guanine to form the activatable cancer theranostic system. The activatable cancer theranostic system is able to recognize MCF-7 cells by aptamer AS1411 and then enter the cells. In the presence of targets, the antisequences in the activatable cancer theranostic system hybridize with intracellular mRNA Bcl-2 and piRNA-36026, leading to the fluorescence signal recovery of Cy3 and Cy5 and the downregulation of two targets in the cytoplasm as well as the consequent apoptosis of MCF-7 cells in the form of gene therapy. Interestingly, as the antisequences are designed in the assembly strands, the hybridization between targets and the antisequences results in the disassembly of the activatable cancer theranostic system and the release of DOX as well as sequential chemotherapy. Advantageously, the activatable cancer theranostic system can achieve imaging of dual cancer-related RNAs with an imaging time window as long as 15 h and exhibit an obvious therapeutic effect in vivo. Therefore, this work is in furtherance of exploration for activatable cancer theranostic systems with high accuracy and efficiency and sheds new light on the development of precision medicine.

Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout

Carbon nanotube (CNT)-based electrodes are cheap, highly performing, and robust platforms for the fabrication of electrochemical sensors. Engineering programmable DNA nanotechnologies on the CNT surface can support the construction of new electrochemical DNA sensors providing an amperometric output in response to biomolecular recognition. This is a significant challenge, since it requires gaining control of specific hybridization processes and functional DNA systems at the interface, while limiting DNA physisorption on the electrode surface, which contributes to nonspecific signal. In this study, we provide design rules to program dynamic DNA structures at the surface of single-walled carbon nanotubes electrodes, showing that specific DNA interactions can be monitored through measurement of the current signal provided by redox-tagged DNA strands. We propose the use of pyrene as a backfilling agent to reduce nonspecific adsorption of reporter DNA strands and demonstrate the controlled formation of DNA duplexes on the electrode surface, which we then apply in the design and conduction of programmable DNA strand displacement reactions. Expanding on this aspect, we report the development of novel amperometric hybridization platforms based on artificial DNA structures templated by the small molecule melamine. These platforms enable dynamic strand exchange reactions orthogonal to conventional toehold-mediated strand displacement and may support new strategies in electrochemical sensing of biomolecular targets, combining the physicochemical properties of nanostructured carbon-based materials with programmable nucleic acid hybridization.

Logic-Gated Proximity Aptasensing for Cell-Surface Real-Time Monitoring of Apoptosis

In nature, intact apoptotic cells release ATP as a signaling molecule to trigger prompt phagocytic clearance, even at the earliest stage of apoptosis. Inspired by this, here we introduce a straightforward strategy for real-time monitoring ATP exocytosis and drug-stimulated apoptosis in the cancer cell surroundings. Triplex-boosted G-quadruplexes (tb-G4s) responding to cell environmental factors (H⁺ and K⁺ ) are engineered to construct a DNA logic-gated nanoplatform for proximity ATP aptasensing on the cell surface. It enables the real-time monitoring of cell apoptosis by capturing released endogenous ATP during chemotherapy drug stimulation, providing a sensitive approach for dynamically evaluating drug-induced apoptosis and therapeutic efficacy.

Non-Coding RNA-Based Biosensors for Early Detection of Liver Cancer

Primary liver cancer is an aggressive, lethal malignancy that ranks as the fourth leading cause of cancer-related death worldwide. Its 5-year mortality rate is estimated to be more than 95%. This significant low survival rate is due to poor diagnosis, which can be referred to as the lack of sufficient and early-stage detection methods. Many liver cancer-associated non-coding RNAs (ncRNAs) have been extensively examined to serve as promising biomarkers for precise diagnostics, prognostics, and the evaluation of the therapeutic progress. For the simple, rapid, and selective ncRNA detection, various nanomaterial-enhanced biosensors have been developed based on electrochemical, optical, and electromechanical detection methods. This review presents ncRNAs as the potential biomarkers for the early-stage diagnosis of liver cancer. Moreover, a comprehensive overview of recent developments in nanobiosensors for liver cancer-related ncRNA detection is provided.

DNA Nanotechnology-Based Biosensors and Therapeutics

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

AI in Measurement Science

Measurement of biological systems containing biomolecules and bioparticles is a key task in the fields of analytical chemistry, biology, and medicine. Driven by the complex nature of biological systems and unprecedented amounts of measurement data, artificial intelligence (AI) in measurement science has rapidly advanced from the use of silicon-based machine learning (ML) for data mining to the development of molecular computing with improved sensitivity and accuracy. This review presents an overview of fundamental ML methodologies and discusses their applications in disease diagnostics, biomarker discovery, and imaging analysis. We next provide the working principles of molecular computing using logic gates and arithmetical devices, which can be employed for in situ detection, computation, and signal transduction for biological systems. This review concludes by summarizing the strengths and limitations of AI-involved biological measurement in fundamental and applied research.

Nucleic Acid Tests for Clinical Translation

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

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Plasmonic sensing of β-glucuronidase activity via silver mirror reaction on gold nanostars

We outline a novel approach for the plasmonic detection of β-glucuronidase activity by modulating the silver mirror reaction at the nanoscale on gold nanostars. β-glucuronidase catalyzes the hydrolysis of a non-reducing substrate to generate reducing products that trigger the silver mirror reaction on gold nanostars to alter their surface plasmon resonance. By modulating the silver deposition on gold nanostars, the unique plasmonic property of silver-coated gold nanostars enables a significant change in the surface plasmon resonance that allows for a plasmonic readout for detecting the enzymatic activity. This plasmonic nanosensor enables a detection of the β-glucuronidase activity as low as 0.1 U/L, showing great promise as a plasmonic approach for enzyme detection.

Flexible sensor based on conducting polymer and gold nanoparticles for electrochemical screening of HPV families in cervical specimens

Considering the low sensitivity of cytological exams and high costs of the molecular methods, the development of diagnostic tests for effective diagnosis of HPV infections is a priority. In this work, biosensor composed of polypyrrole (PPy) films and gold nanoparticles (AuNPs) was obtained for specific detection of HPV genotypes. The biosensor was developed by using flexible electrodes based on polyethylene terephthalate (PET) strips coated with indium tin oxide (ITO). Polymeric films and AuNPs were obtained by electrosynthesis. Oligonucleotides sequences modified with functional amino groups were designed to recognize HPV gene families strictly. The modified oligonucleotides were chemically immobilized on the nanostructured platform. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used for the analysis of the electrode modification and monitoring of molecular hybridization. Electrochemical changes were observed after exposure of the biosensors to plasmid samples and cervical specimens. The biosensor based on the BSH16 probe showed a linear concentration range for target HPV16 gene detection of 100 pg μL^-1 to 1 fg μL^-1. A limit of detection (LOD) of 0.89 pg μL^-1 and limit of quantification (LOQ) of 2.70 pg μL^-1 were obtained, with a regression coefficient of 0.98. Screening tests on cervical specimens were performed to evaluate the sensibility and specificity for HPV and its viral family. The expression of a biomarker for tumorigenesis (p53 gene) was also monitored. In this work, a flexible system has been successfully developed for label-free detection of HPV families and p53 gene monitoring with high specificity, selectivity, and sensitivity.

Boosting biomolecular interactions through DNA origami nano-tailored biosensing interfaces

The interaction between a bioreceptor and its target is key in developing sensitive, specific and robust diagnostic devices. Suboptimal interbioreceptor distances and bioreceptor orientation on the sensor surface, resulting from uncontrolled deposition, impede biomolecular interactions and lead to a decreased biosensor performance. In this work, we studied and implemented a 3D DNA origami design, for the first time comprised of assay specifically tailored anchoring points for the nanostructuring of the bioreceptor layer on the surface of disc-shaped microparticles in the continuous microfluidic environment of the innovative EvalutionTM platform. This bioreceptor immobilization strategy resulted in the formation of a less densely packed surface with reduced steric hindrance and favoured upward orientation. This increased bioreceptor accessibility led to a 4-fold enhanced binding kinetics and a 6-fold increase in binding efficiency compared to a directly immobilized non-DNA origami reference system. Moreover, the DNA origami nanotailored biosensing concept outperformed traditional aptamer coupling with respect to limit of detection (11 × improved) and signal-to-noise ratio (2.5 × improved) in an aptamer-based sandwich bioassay. In conclusion, our results highlight the potential of these DNA origami nanotailored surfaces to improve biomolecular interactions at the sensing surface, thereby increasing the overall performance of biosensing devices. The combination of the intrinsic advantages of DNA origami together with a smart design enables bottom-up nanoscale engineering of the sensor surface, leading towards the next generation of improved diagnostic sensing devices.

Rationally Designed Multivalent Aptamers Targeting Cell Surface for Biomedical Applications

Specific interactions between ligands and receptors on cell surface play an important role in the cell biological process. Nucleic acid aptamers as commonly used ligands enable specific recognition and tight binding to membrane protein receptors for modulation of cell fate. Therefore, molecular probes with aptamers can be applied for cancer diagnosis and targeted therapy by targeting overexpression membrane proteins of cancer cells. However, because of their fast degradation and rapid glomerulus clearance in vivo, the applications of aptamers in physiological conditions remain challenged. Inspired by natural multivalent interactions, many approaches have been developed to construct multivalent aptamers to improve the performance of aptamers in complex matrices with higher binding affinity, more stability, and longer circulation time. In this review, we first introduce the aptamer generation from purified protein-based SELEX and whole cell-based SELEX for targeting the cell surface. We then highlight the approaches to fabricate multivalent aptamers and discuss their properties. By integrating different materials (including inorganic nanomaterials, diacyllipid, polymeric nanoparticles, and DNA nanostructures) as scaffolds with an interface modification technique, we have summarized four kinds of multivalent aptamers. After that, representative applications in biosensing and targeted therapy are illustrated to show the elevated performance of multivalent aptamers. In addition, we analyze the challenges and opportunities for the clinical practices of multivalent aptamers.

DNA Nanostructures in the Fight Against Infectious Diseases

Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.

DNA nanotechnology: A recent advancement in the monitoring of microcystin-LR

The Microcystin-Leucine-Arginine (MC-LR) is the most toxic and widely distributed microcystin, which originates from cyanobacteria produced by water eutrophication. The MC-LR has deleterious effects on the aquatic lives and agriculture, and this highly toxic chemical could severely endanger human health when the polluted food was intaken. Therefore, the monitoring of MC-LR is of vital importance in the fields including environment, food, and public health. Utilizing the complementary base pairing between DNA molecules, DNA nanotechnology can realize the programmable and predictable regulation of DNA molecules. In analytical applications, DNA nanotechnology can be used to detect targets via target-induced conformation change and the nano-assemblies of nucleic acids. Compared with the conventional analytical technologies, DNA nanotechnology has the advantages of sensitive, versatile, and high potential in real-time and on-site applications. According to the molecular basis for recognizing MC-LR, the strategies of applying DNA nanotechnology in the MC-LR monitoring are divided into two categories in this review: DNA as a recognition element and DNA-assisted signal processing. This paper introduces state-of-the-art analytical methods for the detection of MC-LR based on DNA nanotechnology and provides critical perspectives on the challenges and development in this field.

Nuclease resistance of DNA nanostructures

DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.

The Application of Artificial Intelligence in the Genetic Study of Alzheimer's Disease

Alzheimer's disease (AD) is a neurodegenerative disease in which genetic factors contribute approximately 70% of etiological effects. Studies have found many significant genetic and environmental factors, but the pathogenesis of AD is still unclear. With the application of microarray and next-generation sequencing technologies, research using genetic data has shown explosive growth. In addition to conventional statistical methods for the processing of these data, artificial intelligence (AI) technology shows obvious advantages in analyzing such complex projects. This article first briefly reviews the application of AI technology in medicine and the current status of genetic research in AD. Then, a comprehensive review is focused on the application of AI in the genetic research of AD, including the diagnosis and prognosis of AD based on genetic data, the analysis of genetic variation, gene expression profile, gene-gene interaction in AD, and genetic analysis of AD based on a knowledge base. Although many studies have yielded some meaningful results, they are still in a preliminary stage. The main shortcomings include the limitations of the databases, failing to take advantage of AI to conduct a systematic biology analysis of multilevel databases, and lack of a theoretical framework for the analysis results. Finally, we outlook the direction of future development. It is crucial to develop high quality, comprehensive, large sample size, data sharing resources; a multi-level system biology AI analysis strategy is one of the development directions, and computational creativity may play a role in theory model building, verification, and designing new intervention protocols for AD.

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.

Surface plasmon resonance assay for exosomes based on aptamer recognition and polydopamine-functionalized gold nanoparticles for signal amplification

A novel surface plasmon resonance (SPR) strategy is introduced for the specific determination of exosomes based on aptamer recognition and polydopamine-functionalized gold nanoparticle (Au@PDA NP)-assisted signal amplification. Exosomes derived from hepatic carcinoma SMMC-7721 were selected as the model target. SMMC-7721 exosomes can be specifically captured by the aptamer ZY-sls that was complementary to the DNA tetrahedron probes (DTPs), and then the CD63 aptamer-linked Au@PDA NPs recognized SMMC-7721 exosomes for signal amplification. The DTPs were modified on a Au film for preventing Au deposition on the surface during the introduction of HAuCl₄, and PDA coated on the AuNPs was used to reduce HAuCl₄ in situ without any reductant assistance. It results in a further enhanced SPR signal. The assay can clearly distinguish SMMC-7721 exosomes from others (HepG2 exosomes, Bel-7404 exosomes, L02 exosomes, MCF-7 exosomes, and SW480 exosomes, respectively). SMMC-7721 exosomes are specifically determined as low as 5.6 × 10⁵ particles mL^-1. The method has successfully achieved specific determination of SMMC-7721 exosomes even in 50% of human serum without any pretreatment. Graphical abstract A novel surface plasmon resonance (SPR) strategy was introduced for the specific determination of exosomes based on aptamer recognition and polydopamine functionalized gold nanoparticles (Au@PDA NPs). The SPR signal was improved using the Au@PDA NPs assisted amplification.

Multi-targeted Antisense Oligonucleotide Delivery by a Framework Nucleic Acid for Inhibiting Biofilm Formation and Virulence

A framework nucleic acid delivery system was developed through self-assembly, which can deliver antisense oligonucleotides against multiple targets in bacterial cells.

The ASOs-tFNAs (750 nM) was found to simultaneously inhibit the expression of gtfBCD, gbpB, and ftf, and significantly reduce the extracellular polysaccharide synthesis and biofilm thickness.

Biofilm formation is responsible for numerous chronic infections and represents a serious health challenge. Bacteria and the extracellular polysaccharides (EPS) cause biofilms to become adherent, toxic, resistant to antibiotics, and ultimately difficult to remove. Inhibition of EPS synthesis can prevent the formation of bacterial biofilms, reduce their robustness, and promote removal. Here, we have developed a framework nucleic acid delivery system with a tetrahedral configuration. It can easily access bacterial cells and functions by delivering antisense oligonucleotides that target specific genes. We designed antisense oligonucleotide sequences with multiple targets based on conserved regions of the VicK protein-binding site. Once delivered to bacterial cells, they significantly decreased EPS synthesis and biofilm thickness. Compared to existing approaches, this system is highly efficacious because it simultaneously reduces the expression of all targeted genes (gtfBCD, gbpB, ftf). We demonstrate a novel nucleic acid-based nanomaterial with multi-targeted inhibition that has great potential for the treatment of chronic infections caused by biofilms.

Tailoring DNA Self-assembly to Build Hydrogels

DNA hydrogels are crosslinked polymeric networks in which DNA is used as the backbone or the crosslinker. These hydrogels are novel biofunctional materials that possess the biological character of DNA and the framed structure of hydrogels. Compared with other kinds of hydrogels, DNA hydrogels exhibit not only high mechanical strength and controllable morphologies but also good recognition ability, designable responsiveness, and programmability. The DNA used in this type of hydrogel acts as a building block for self-assembly or as a responsive element due to its sequence recognition ability and switchable structural transitions, respectively. In this review, we describe recent developments in the field of DNA hydrogels and discuss the role played by DNA in these hydrogels. Various synthetic strategies for and a range of applications of DNA hydrogels are detailed.

Target induced framework nucleic acid nanomachine with doxorubicin-spherical nucleic acid tags for electrochemical determination of human telomerase activity

A stable and enzyme-free method is described for highly sensitive determination of telomerase activity. It is based on the use of a framework nucleic acid (FNA) nanomachine and doxorubicin-spherical nucleic acid (DSNA) tags. Upon incubation with telomerase, the primer-tetrahedron becomes elongated to form the handed swing arm. The extended swing arm autonomously moves along the predefined track consisting of entropy-tetrahedron by consecutive strand displacement under the aid of fuel-tetrahedron. As a result, many (entropy-tetrahedron)-(fuel-tetrahedron) complexes are assembled for combining the DSNA tags. This results in an amplified electrochemical signal, typically measured at around -0.63 V (Ag/AgCl). The use of an enzyme-free FNA nanomachine and of DSNA tags warrants outstandingly high stability and sensitivity. The method shows a broad dynamic correlation of telomerase activity in cell extracts. The analytical range extends from 10 to 1.0 × 10⁴ HeLa cells mL^-1 with a lower detection limit of 2 cells mL^-1. The differences in telomerase activity between different cancer cells can be easily evaluated. The method was further verified by quantifying telomerase activity of cancer cells in accumulated normal cells. Therefore, the sensing method has great potential for clinical application. Graphical abstractSchematic representation of the electrochemical biosensor based on target induced framework nucleic acid nanomachine with doxorubicin-spherical nucleic acids (DSNA) tags, which can be used to the determination of telomerase activity in accumulated normal cells. dNTP: Deoxynucleotide triphosphates; FT: Fuel-tetrahedron.

ATP-Triggered, Allosteric Self-Assembly of DNA Nanostructures

Responsive self-assembly is a general process in biological systems and is highly desired in engineered systems. DNA nanostructures provide a versatile molecular platform for studying such responsive self-assembly. Various triggers have been explored for DNA nanostructures. However, each trigger requires a unique mechanism for its response. This situation brings a great challenge to engineer the responsiveness. Herein, we propose an aptamer-based, allosteric mechanism for responsive DNA self-assembly. The aptamer-ligand binding causes the DNA motif to change its conformation and thus influences the motif assembly. With a model of an ATP aptamer, we have demonstrated the responsive assembly. Such responsive behavior, we believe, will be an important element for molecular machines, bioimaging/biosensing, and drug delivery.

The Fusion of Lipid and DNA Nanotechnology

Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological process that is facilitated by a diverse range of membrane proteins, including ion-channels and pores. However, biological membranes and their associated proteins are challenging to experimentally characterize. These challenges have motivated recent advances in nanotechnology towards building and manipulating synthetic lipid systems. Liposomes-aqueous droplets enclosed by a bilayer membrane-can be synthesised in vitro and used as a synthetic model for the cell membrane. In DNA nanotechnology, DNA is used as programmable building material for self-assembling biocompatible nanostructures. DNA nanostructures can be functionalised with hydrophobic chemical modifications, which bind to or bridge lipid membranes. Here, we review approaches that combine techniques from lipid and DNA nanotechnology to engineer the topography, permeability, and surface interactions of membranes, and to direct the fusion and formation of liposomes. These approaches have been used to study the properties of membrane proteins, to build biosensors, and as a pathway towards assembling synthetic multicellular systems.

DNA nanotechnology approaches for microRNA detection and diagnosis

MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.