Dynamic colloidal nanoparticle assembly triggered by aptamer-receptor interactions on live cell membranes

DNA-mediated precise regulation of SERS hotspots for biosensing and bioimaging

Surface-enhanced Raman scattering (SERS) is a powerful analytical technique, where the creation of "hotspots" holds the key to unlocking sensitive, reproducible and reliable performance. DNA nanostructures, known for their unique predictability and exceptional programmability, have emerged as promising tools for the controllable assembly and precise regulation of SERS hotspots. In recent years, the application of DNA nanotechnology in the regulation of SERS hotspots has emerged as a research focus, but a comprehensive summary of this field is still lacking. This review begins by elucidating the mechanisms of localized surface plasmon resonance (LSPR) coupling and SERS enhancement, providing a theoretical foundation for the design principles and assembly strategies for SERS hotspots. Following this, general approaches for assembling static SERS hotspots using DNA structures of different dimensions as linkers or templates are explored. Subsequently, we delve into dynamic regulation strategies for SERS hotspots mediated by DNA structures, focusing on structural reconfiguration driven by DNA hybridization, toehold-mediated strand displacement (TMSD), and enzyme-catalyzed DNA allostery, and then summarize recent examples of DNA-mediated hotspot regulation in biosensing and bioimaging applications. Finally, we discuss future perspectives associated with the DNA-mediated precise regulation of SERS hotspots, underscoring the imperative for enhanced scalability, uniformity, and integration to pave the way for real-world applications.

Artificial molecular motors in biological applications

Molecular motors are the cornerstone for the maintenance of living systems and mediate almost all fundamental processes involved in cellular trafficking. The intricate mechanisms underlying natural molecular motors have been elucidated in detail, inspiring researchers in various fields to construct artificial systems with multi-domain applications. This review summarises the characteristics of molecular motors, biomimetic approaches for their design and operation, and recent biological applications.

Tailoring strategies of SERS tags-based sensors for cellular molecules detection and imaging

As an emerging nanoprobe, surface enhanced Raman scattering (SERS) tags hold significant promise in sensing and bioimaging applications due to their attractive merits of anti-photobleaching ability, high sensitivity and specificity, multiplex, and low background capabilities. Recently, several reviews have proposed the application of SERS tags in different fields, however, the specific sensing strategies of SERS tags-based sensors for cellular molecules have not yet been systematically summarized. To provide beneficial and comprehensive insights into the advanced SERS tags technique at the cellular level, this review systematically elaborated on the latest advances in SERS tags-based sensors for cellular molecules detection and imaging. The general SERS tags-based sensing strategies for biomolecules and ions were first introduced according to molecular classes. Then, aiming at such molecules located in the extracellular, cellular membrane and intracellular regions, the tailored strategies by designing and manipulating SERS tags were summarized and explored through several key examples. Finally, the challenges and perspectives of developing high performance of advanced SERS tags were briefly discussed to provide effective guidance for further development and extended applications.

Engineering Assembly of Plasmonic Virus-Like Gold SERS Nanoprobe Guided by Intelligent Dual-Machine Nanodevice for High-Performance Analysis of Tetracycline

Accurate detection of trace tetracyclines (TCs) in complex matrices is of great significance for food and environmental safety monitoring. However, traditional recognition and amplification tools exhibit poor specificity and sensitivity. Herein, a novel dual-machine linkage nanodevice (DMLD) is proposed for the first time to achieve high-performance analysis of TC, with a padlock aptamer component as the initiation command center, nucleic acid-encoded multispike virus-like Au nanoparticles (nMVANs) as the signal indicator, and cascade walkers circuit as the processor. The existence of spike vertices and interspike nanogaps in MVANs enables intense electromagnetic near-field focusing, allowing distinct surface-enhanced Raman scattering (SERS) activity. Moreover, through the sequential activation between multistage walker catalytic circuits, the DLMD system converts the limited TC recognition into massive engineering assemblies of SERS probes guided by DNA amplicons, resulting in synergistic enhancement of bulk plasmonic hotspot entities. The continuously guaranteed target recognition and progressively promoted signal enhancement ensure highly specific amplification analysis of TC, with a detection limit as low as 7.94 × 10-16 g mL-1. Furthermore, the reliable recoveries in real samples confirm the practicability of the proposed sensing platform, highlighting the enormous potential of intelligent nanomachines for analyzing the trace hazards in the environment and food.

A spatially localized DNA linear classifier for cancer diagnosis

Molecular computing is an emerging paradigm that plays an essential role in data storage, bio-computation, and clinical diagnosis with the future trends of more efficient computing scheme, higher modularity with scaled-up circuity and stronger tolerance of corrupted inputs in a complex environment. Towards these goals, we construct a spatially localized, DNA integrated circuits-based classifier (DNA IC-CLA) that can perform neuromorphic architecture-based computation at a molecular level for medical diagnosis. The DNA-based classifier employs a two-dimensional DNA origami as the framework and localized processing modules as the in-frame computing core to execute arithmetic operations (e.g. multiplication, addition, subtraction) for efficient linear classification of complex patterns of miRNA inputs. We demonstrate that the DNA IC-CLA enables accurate cancer diagnosis in a faster (about 3 h) and more effective manner in synthetic and clinical samples compared to those of the traditional freely diffusible DNA circuits. We believe that this all-in-one DNA-based classifier can exhibit more applications in biocomputing in cells and medical diagnostics.

DNA-Based Fluorescent Nanoprobe for Cancer Cell Membrane Imaging

As an important barrier between the cytoplasm and the microenvironment of the cell, the cell membrane is essential for the maintenance of normal cellular physiological activities. An abnormal cell membrane is a crucial symbol of body dysfunction and the occurrence of variant diseases; therefore, the visualization and monitoring of biomolecules associated with cell membranes and disease markers are of utmost importance in revealing the biological functions of cell membranes. Due to their biocompatibility, programmability, and modifiability, DNA nanomaterials have become increasingly popular in cell fluorescence imaging in recent years. In addition, DNA nanomaterials can be combined with the cell membrane in a specific manner to enable the real-time imaging of signal molecules on the cell membrane, allowing for the real-time monitoring of disease occurrence and progression. This article examines the recent application of DNA nanomaterials for fluorescence imaging on cell membranes. First, we present the conditions for imaging DNA nanomaterials in the cell membrane microenvironment, such as the ATP, pH, etc. Second, we summarize the imaging applications of cell membrane receptors and other molecules. Finally, some difficulties and challenges associated with DNA nanomaterials in the imaging of cell membranes are presented.

Dual Biomimetic Recognition-Driven Plasmonic Nanogap-Enhanced Raman Scattering for Ultrasensitive Protein Fingerprinting and Quantitation

Protein assays with fingerprints and high sensitivity are essential for biomedical research and applications. However, the prevailing methods mainly rely on indirect or labeled immunoassays, failing to provide fingerprint information. Herein, we report a dual biomimetic recognition-driven plasmonic nanogap-enhanced Raman scattering (DBR-PNERS) strategy for ultrasensitive protein fingerprinting and quantitation. A pair of molecularly imprinted nanoantennas were rationally engineered for specifically trapping a target protein into well-defined plasmonic nanogaps through dual-terminal recognition for ultrahigh Raman signal amplification. Meanwhile, a Raman-active small molecule was embedded into the nanoantenna as an internal standard to provide a ratiometric assay for robust quantitation. DBR-PNERS exhibited several significant merits over existing approaches, including fingerprinting, ultrahigh sensitivity, quantitation robustness, speed, sample consumption, and so on. Therefore, it can be a promising tool for a protein assay and holds a great perspective in important applications.

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.

[Separation and enrichment of trace aflatoxin B1 in grains by magnetic nanomaterials based on SiO2@Fe3O4]

In this study, a magnetic nanomaterial antibody (Ab)-SiO2@Fe3O4 was synthesized, which was employed to absorb aflatoxin B1 (AFB1) in complicated grain matrices. The Ab-SiO2@Fe3O4 material was then paired with high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) for subsequent accurate detection. The Ab-SiO2@Fe3O4 material has a specific adsorption capacity for AFB1 because of the stable and specific biological binding between antigen and antibody. This process can achieve the identification between the material and food matrix quickly, thereby completing the separation and enrichment process. Then, high sensitivity and high accuracy HPLC-MS/MS were employed for signal readout and actual quantification, which can significantly increase the detection efficiency and enable high-throughput detection of numerous samples. In the pretreatment process, Fe3O4 was first synthesized by microwave-assisted hydrothermal synthesis within 1 h, and Ab-SiO2@Fe3O4 was then produced using the enhanced Stober's approach. This material with high adsorption performance was synthesized under relatively mild conditions and short time. To obtain Ab-SiO2@Fe3O4 materials with uniform particle size, magnetic properties, and dispersibility that met the requirements, synthesis conditions of Ab-SiO2@Fe3O4 and conditions for capturing the AFB1 target were analyzed. The findings demonstrated that the best effect was obtained when the dosage of FeCl3·6H2O was 10.0 mmol, the heating time was 40 min, and 100 μL tetraethoxysilane was employed for SiO2 coating. The AFB1 antibody was then combined with the surface of SiO2@Fe3O4 under several conditions. The findings revealed that the best coupling efficiency of Ab could be obtained when the concentration of 2-morpholinoethanesulfonic acid monohydrate (MES) was 10 mmol/L, pH was 6.5, and the molar ratio of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC)∶N-hydroxysuccinimide substances (NHS) was 2∶1. The coupling buffer was then selected as phosphate buffer (PBS) with pH=7.4, and 8 mg Ab-SiO2@Fe3O4 was employed to separate and enrich AFB1 at 37 ℃ for 10 min. In the actual detection, acetonitrile-water-formic acid (85∶10∶5, v/v/v) was employed as the extraction solution. After ultrasonic extraction for 10 min, Ab-SiO2@Fe3O4 was employed to separate and enrich AFB1 in the extract. The supernatant was dried with nitrogen and reconstituted with 1-mL acetonitrile. The solution was then filtered through a 0.22 μm filter and detected using HPLC-MS/MS, thereby realizing the quick and quantitative detection of AFB1. AFB1 had an excellent linear relationship in the range of 2-50 μg/L under the optimal analytical conditions, and the correlation coefficient was less than 0.99. The LOD was 0.04 μg/kg, and the LOQ was 0.13 μg/kg. The spiked recoveries of AFB1 in three grain matrices ranged from 76.21% to 92.85% with RSD≤5.29% at four different spiked levels. The approach was applied to the determination and analysis of AFB1 in 30 real grain samples of rice, corn, and wheat. The findings demonstrated that AFB1 was detected in one wheat sample and two corn samples, and its content was 0.38, 0.13, and 0.47 μg/kg, respectively, and no toxins were found in other samples. The approach combined Ab-SiO2@Fe3O4 magnetic nanomaterials with HPLC-MS/MS, which could obtain high-efficiency separation and enrichment of AFB1. Furthermore, the low-cost Ab-SiO2@Fe3O4 could be stored for more than a week and complete the pretreatment process within 30 min. This effective pretreatment process combined with HPLC-MS/MS could realize the analysis of several samples within a short time, and had a promising application prospect in the detection of AFB1 in grains.

Assembling of anisotropic plasmonic sheet-core-satellites for simultaneous ultrasensitive detection of MC-LR toxin

An anisotropic plasmonic sheet-core-satellite (PSCS) superstructure can be controlled via competitive binding between aptamer/MC-LR conjugation and aptamer-ssDNA hybridization. SERS nanotags can be incorporated into anisotropic plasmonic sheet-cores, e.g., pGO/nanorods, or pGO/hollow AgCl : Au nanoplates so as to fabricate an aptasensor for "ON-OFF" detection of MC-LR toxin. Preparing a PSCS superstructure and detection of toxin can be simultaneously completed so as to simplify the detection procedure of MC-LR toxin. Detection sensitivity of MC-LR toxin can be optimized by controlling aspect ratios or hollow interiors of plasmonic core nanoparticles. Herein, a limit of detection (0.635 pM) with a wide linear range from 1 pM to 10 nM can be obtained via optimized PSCS of pGO/nanorod/dotnanotags. When the aptasensor was tested in real samples, the PSCS shows excellent recoveries from 96.6% to 104.5% with relative standard deviation (RSD) lower than 2.89% in spiked reservoir samples. It can be predicted that a one-step facile nanofabrication/aptasensing approach would be extensively applied for rapid detection of some other environmental contaminants.

Many Birds, One Stone: A Smart Nanodevice for Ratiometric Dual-Spectrum Assay of Intracellular MicroRNA and Multimodal Synergetic Cancer Therapy

The development of a theragnostic platform integrating precise diagnosis and effective treatment is significant but still extremely challenging. Herein, an integrated smart nanodevice composed of Au@Cu_2-xS@polydopamine nanoparticles (ACSPs) and fuel DNA-conjugated tetrahedral DNA nanostructures (fTDNs) was constructed, in which the ACSP nanoprobe played multiple key roles in antitumor therapy as well as in situ monitoring of microRNAs (miRNAs) in cancer cells. Regarding the analysis, the ACSP probe contained two optical properties: excellent surface-enhanced Raman scattering (SERS) enhancement and high fluorescence (FL) quenching performance. Employing the ACSPs as the high-efficiency detection substrate combined with the fTDN-assisted DNA walking nanomachines as the superior amplification strategy, a SERS-FL dual-spectrum biosensor was constructed, which achieved an ultralow background signal and excellent sensitivity with detection limits of 0.11 pM and 4.95 aM by FL and SERS, respectively. Moreover, the rapid FL imaging and precise SERS quantitative detection for miRNA in cancer cells were also achieved by dual-signal ratio strategy, improving the accuracy of diagnosis. Regarding the therapeutic application, due to the high reactive oxygen species generation ability and excellent photothermal conversion efficiency, the ACSPs can also act as an all-in-one nanoagent for multimodal collaborative tumor therapy. Significantly, both in vivo and in vitro experiments confirmed its high biological safety and strong anticancer effect, indicating its promising theragnostic applications.

Microfluidic synthesis of high-valence programmable atom-like nanoparticles for reliable sensing

Synthesis of programmable atom-like nanoparticles (PANs) with high valences and high yields remains a grand challenge. Here, a novel synthetic strategy of microfluidic galvanic displacement (μ-GD) coupled with microfluidic DNA nanoassembly is advanced for synthesis of single-stranded DNA encoder (SSE)-encoded PANs for reliable surface-enhanced Raman scattering (SERS) sensing. Notably, PANs with high valences (e.g., n-valence, n = 12) are synthesized with high yields (e.g., >80%) owing to the effective control of interfacial reactions sequentially occurring in the microfluidic system. On the basis of this, we present the first demonstration of a PAN-based automatic analytical platform, in which sensor construction, sample loading and on-line monitoring are carried out in the microfluidic system, thus guaranteeing reliable quantitative measurement. In the proof-of-concept demonstration, accurate determination of tetracycline (TET) in serum and milk samples with a high recovery close to 100% and a low relative standard deviation (RSD) less than 5.0% is achieved by using this integrated analytical platform.

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.

Label-free amplified fluorescence detection of DNA biomarkers based on KFP polymerase-driven double strand displacement reactions and magnetic nanoprobes

Developing a sensitive, low-cost and general sensing platform for the analysis of a DNA biomarker and its mutation is important for early cancer screening. In our work, the tumor suppressor gene-p53 DNA was chosen as the model DNA biomarker due to its vital role in preventing oncogene cancer-inhibiting activity through mediating cellular proliferation and apoptosis. Compared with tumor biopsy, the quantification of p53 DNA and its mutation in biofluids (such as urine) is more convenient due to its simple operation and non-invasiveness. Herein, a label-free amplified fluorescence assay has been developed for p53 DNA in urine samples through the KFP polymerase-driven double strand displacement reactions and a magnetic nanoprobe. First, the ssDNA probe (RP) was designed with antisense sequences for p53 DNA and the Nb.BbvCI endonuclease recognition site. In the presence of p53 DNA, the formed dsDNA between RP and p53 DNA served as an engaging primer to initiate the first strand displacement reaction (SDA) under the action of KFP DNA polymerase and Nb.BbvCI, generating abundant short ssDNA (primer). Subsequently, the resulting primers will initiate the downstream SDA through the primer-hairpin DNA (HPa) binding, opening up, and extension of HPb and HPc under the action of KFP DNA polymerase. In the process of this final DNA polymerization reaction, the primer hybridized on HPa is released and goes on to initiate another round, forming plenty of duplex Y-shaped DNA. With the integration of SYBR Green I (SG I) into these duplex DNA, the amplified label-free fluorescence detection platform for p53 DNA can be achieved. Moreover, a biotin modified nanoprobe (bio-CP) was used to capture the superfluous HP. By performing the separation function, the binding of superfluous HP and SG could be avoided and a low background can be acquired. Benefiting from the abundant SG intercalation sites of Y-shaped DNA and low background signals, this method showed excellent sensitivity with a detection limit of 0.012 nM, and the p53 DNA in urine samples was evaluated, offering a powerful tool for biomedical research and clinical diagnosis.

Synthesis of AB n -type colloidal molecules by polymerization-induced particle-assembly (PIPA)

Conventional synthesis of colloidal molecules (CMs) mainly depends on particle-based self-assembly of patchy building blocks. However, direct access to CMs by the self-assembly of isotropic colloidal subunits remains challenging. Here, we report the mass production of AB n -type CMs by polymerization-induced particle-assembly (PIPA), using a linear ABC triblock terpolymer system. Starting from diblock copolymer spheres, the association of spheres takes place in situ during the polymerization of the third block. The third blocks aggregate into attractive domains, which connect spheres into CMs. The stability of CMs is ensured, as long as the conversions are limited to ca. 50%, and the pH is low. The valence of AB n -type CMs (n = 2-6) is determined by the volume ratio of the polymer blocks. By tuning the volume ratio, 78.5% linear AB2-type CMs are yielded. We demonstrate that polymerization-induced particle-assembly is successful for the scalable fabrication of AB n -type CMs (50 g L-1), and can be easily extended to vastly different triblock terpolymers, for a wide range of applications.

Capture and selective release of multiple types of circulating tumor cells using smart DNAzyme probes

The effective capture, release and reanalysis of circulating tumor cells (CTCs) are of great significance to acquire tumor information and promote the progress of tumor therapy. Particularly, the selective release of multiple types of CTCs is critical to further study; however, it is still a great challenge. To meet this challenge, we designed a smart DNAzyme probe-based platform. By combining multiple targeting aptamers and multiple metal ion responsive DNAzymes, efficient capture and selective release of multiple types CTCs were realized. Sgc8c aptamer integrated Cu2+-dependent DNAzyme and TD05 aptamer integrated Mg2+-dependent DNAzyme can capture CCRF-CEM cells and Ramos cells respectively on the substrate. With the addition of Cu2+ or Mg2+, CCRF-CEM cells or Ramos cells will be released from the substrate with specific selectivity. Furthermore, our platform has been successfully demonstrated in the whole blood sample. Therefore, our capture/release platform will benefit research on the molecular analysis of CTCs after release and has great potential for cancer diagnosis and individualized treatment.