Freezing Directed Construction of Bio/Nano Interfaces: Reagentless Conjugation, Denser Spherical Nucleic Acids, and Better Nanoflares

Cathepsin B-induced cascade DNA-AuNP nanomachine for activated tumor theranostics

Since targeted and efficient accumulation of nanoparticles into tumors is essential for accurate cancer theranostics, spatiotemporally controlling the aggregation of small nanoparticles (such as gold nanoparticles, AuNPs) in the tumor microenvironment holds significant promise for improving the diagnostic and therapeutic efficiency against tumors. Here, we introduce a cascade DNA-AuNP nanomachine (CNM) that can in situ magnify the protease-catalyzed peptide cleavage via DNA amplification machinery for cathepsin B (Cat B) activity imaging and Cat B-responsive photothermal therapy of tumors. The CNM is composed of a nanomediator formed by tethering a mediator DNA/peptide complex on AuNPs (DpAuNP) and a nanoeffector consisted of AuNPs and DNA modules (DNA-AuNP). In the cascade, Cat B-mediated peptide cleavage of mediator DNA/peptide complex on DpAuNPs initiates both the detachment of fluorescent DNA reporter from DNA-AuNPs for Cat B imaging and the aggregation of AuNPs for tumor photothermal therapy via toehold-mediated stand displacement (TMSD) reaction. Our results demonstrate that the CNM not only offers superior sensitivity and specificity for Cat B imaging, but also facilitates the activated aggregation of AuNPs for enhanced photothermal therapy of tumors. This CNM represents a Cat B-specific sense-and-treat paradigm for cancer theranostics.

Chiroptical hybrid nanomaterials based on metal nanoparticles and biomolecules

Chirality at the nanoscale has recently attracted renewed attention from the scientific community. As a result, various strategies have been proposed to develop chiral nanomaterials based on metal nanoparticles and chiral biomolecules such as DNA, amino acids, or proteins. We review herein the past and recent literature related to the functionalization of metal nanoparticles with various chiral biomolecules and their assembly into biomaterials with chiroptical response. We divide the review into two main parts, according to the class of biomolecules. We first discuss mechanisms employed to obtain chiral bioconjugates based on metal nanoparticles and amino acids or their derivatives (peptides and proteins), including mechanisms for chirality transfer from chiral biomolecules to achiral nanoparticles. We also review the use of amino acids/peptides as either chiral inducers for the growth of chiral nanoparticles or templates for the chiral arrangement of achiral nanoparticles. In the second part we present an overview of methods to prepare bioconjugates comprising DNA and metal nanoparticles, as well as selected examples of helical nanoparticle arrangements that employ DNA as a chiral template.

Freezing-assisted and affinity-mediated conjugation strategy: Boosting protein loading on gold nanoparticles for enhanced immunoassay performance

Protein-conjugated gold nanoparticles (protein-Au NPs) have been extensively applied in the field of biochemistry due to their unique properties. It is of great significance to regulate the protein loading, reduce the loss of protein activity, and enhance the stability and accessibility of protein-Au NPs for their biochemical application. Herein, we investigated the freezing-assisted strategy for binding proteins to Au NPs, which was effective for various proteins and Au NPs with different sizes. The protein-Au NPs prepared by this freezing strategy exhibited better stability and higher protein loading compared to those prepared by typical direct adsorption (shaking) strategy. Based on this, we proposed a freezing-assisted and affinity-mediated strategy to conjugate proteins to Au NPs. In this strategy, biotinylated BSA (BSA-Bio) was employed as a mediator to bind protein to Au NPs through bioaffinity interaction. By attaching streptavidin-conjugated HRP (SA-HRP) onto Au NPs in this way, a nanoparticle denoted as Au NPs@BSA-Bio@SA-HRP was obtained. And we discovered that the protein loading of this nanoparticle prepared with 68 nm Au NPs was astonishingly 253 times higher than that of shaking strategy under the same conditions. In view of the advantages of this freezing-assisted and affinity-mediated strategy, we prepared antibody- and BSA-Bio-conjugated Au NPs for the immunoassay of interleukin-6 (IL-6). A limit of detection of 3.39 pg/mL was achieved, which was 7.4 times more sensitive than the conventional method. This study offered a new insight for protein conjugation and demonstrated a great potential for practical applications.

Gold Nanoparticles Coated with Nucleic Acids: An Overview of the Different Bioconjugation Pathways

Gold-based nanomaterials have marked the last few decades with the emergence of new medical technologies presenting unique features. For instance, the conjugation of gold nanoparticles (AuNPs) and nucleic acids has allowed the creation of nanocarriers with immense promise for gene therapy applications. Although the use of lipid particles as RNA delivery vectors has been broadly explored, this review aims to focus on the limited models reported for the conjugation of RNA with AuNPs. This is nonetheless unexpected regarding the manifold strategies existing to conjugate DNA to gold nanoparticles, which are exhaustively listed in this paper. Furthermore, new processes such as fast microwave and freezing methods have been described very recently, and it therefore seemed necessary to review these recent but promising conjugation pathways and to pick out those applicable to RNA. Indeed, RNA is considerably more attractive than DNA for therapeutic purposes, but its low stability involves numerous difficulties in the construction of effective nanodevices. However, from the many approaches developed for DNA, it turns out that just two of them are frequently used for the building of RNA delivery platforms based on gold: the salt-aging method with thiolated RNA strands and physisorption. However, both approaches present strong limitations such as the low stability of the Au-S bond and the potential cytotoxicity of polycations. To conclude, this general assessment highlights that the exploration of innovating approaches implying different chemistries is needed for the creation of more robust and shapeable AuNPs-RNA conjugates.

Thermus thermophilus Argonaute-Mediated Single Particle Counting Platform for Multiplex Cancer-Related Biomarkers Detection

The clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) system has achieved remarkable success in the field of nucleic acid detection, while its Achilles' heel lies in the difficulties encountered in flexibility regarding the multiplex detection. As a sister system of CRISPR-Cas, prokaryotic Argonautes (pAgos) have precise recognition, multiturnover, and more importantly multiple specific cleavage characteristics, which is a potential candidate for the next generation of multiplex detection. Herein, a single particle counting platform was developed for the simultaneous detection of three colorectal cancer-related miRNAs (miR-141, miR-31, and miR-21) by combining single particle inductively coupled plasma mass spectrometry (SP-ICPMS) with the Thermus thermophilus Argonaute protein (TtAgo), with nanoparticles as signal probes for cleavage. The platform demonstrated high sensitivity (aM level) and specificity due to the dual-cycle mechanism of exponential isothermal amplification (EXPAR) and TtAgo cleavage, as well as the combination of TtAgo's specific cleavage capability and the multiplex detection advantages of metal stable isotope tagging. Additionally, the platform showed good robustness in human serum and cell extracts, indicating significant potential in clinical applications.

Construction of a Ligation-Controlled Single-Molecule Biosensor for Simultaneous Measurement of Multiple Cancer-Related circRNAs in Clinical Tissues

Circular RNAs (circRNAs) are noncoding RNAs with covalently closed circular structures that regulate important cellular processes, and their dysregulation is implicated in the pathogenesis and progression of various cancers. Simultaneous and specific detection of multiple circRNAs is of significant importance in the early diagnosis of cancer. Herein, we develop a ligation-controlled single-molecule biosensor for multiplexed measurement of breast cancer-associated circRNAs. This assay integrates the isothermal exponential amplification reaction (EXPAR)-induced generation of multiple DNAzymes with a Au nanoparticle (AuNP)-based spherical nucleic acid nanoprobe. The back-splice junction (BSJ) sequences of circFOXO3 and circMTO1 can serve as the templates to ligate their hairpin probes and helper probes under the catalysis of SplintR ligase, forming complete amplification templates. Afterward, the ligated amplification template can serve as both a primer and a template to initiate the EXPAR, inducing the exponential accumulation of characteristic DNAzyme sequences (i.e., DNAzymes 1 and 2). DNAzymes 1 and 2 can be paired with signal probes 1 and 2 immobilized on the AuNP surface, respectively, inducing cyclic degradation of signal probes to liberate large amounts of Cy5 and Cy3 fluorophores and achieving detection limits of 8.34 aM for circFOXO3 and 9.84 aM for circMTO1. This single-molecule biosensor has been successfully applied for simultaneous analysis of multiple circRNAs in a single cancer cell and differentiation of multiple circRNA levels between breast cancer tissues and healthy para-carcinoma tissues, offering a new paradigm for biomedical research and circRNA-related molecular diagnostics.

A CRISPR/Cas12a-Assisted SERS Nanosensor for Highly Sensitive Detection of HPV DNA

The lack of timely and effective screening and diagnosis is a major contributing factor to the high mortality rate of cervical cancer in low-income countries and resource-limited regions. Therefore, the development of a rapid, sensitive, and easily deployable diagnostic tool for HPV DNA is of critical importance. In this study, we present a novel high-sensitivity and high-specificity detection method for HPV16 and HPV18 by integrating the CRISPR/Cas12a system with surface-enhanced Raman scattering (SERS) technology. This method leverages the trans-cleavage activity of the CRISPR/Cas12a system, which cleaves biotin-modified spherical nucleic acids (Biotin-SNA) in the presence of target DNA, releasing free Biotin-DNA. The released Biotin-DNA preferentially binds to streptavidin-modified magnetic beads (SAV-MB), reducing the capture of Biotin-SNA by SAV-MB and thereby significantly enhancing detection sensitivity. This method offers the potential for point-of-care diagnostics as it operates efficiently at 37 °C without the need for thermal cycling. Using standard DNA samples, we demonstrated that this biosensor achieved detection limits as low as 209 copies/μL and 444 copies/μL within 95 min. When combined with recombinase polymerase amplification (RPA), the sensor demonstrated enhanced sensitivity, enabling detection of target DNA at concentrations as low as 1 copy/μL within approximately 50 min. Furthermore, validation with clinical samples confirmed the feasibility and practical applicability of this method. This novel SERS-based sensor offers a new and effective tool in the prevention and detection of cervical cancer.

Spherical Nucleic Acids Meet Acoustic Levitation: A Breakthrough in Synthesis and Application

Spherical nucleic acids (SNAs), with their densely packed nucleic acid shells and programmable functionalities, have become indispensable in nanomedicine and biosensing. Developed synthesis methods, including salt aging, pH modulation, freeze-thaw cycling, n-butanol dehydration, evaporation drying, and microwave heating, have enabled foundational advances but are constrained by slow kinetics, compromised structural uniformity and especially harsh reaction conditions, making them unsuitable for in situ tracking of biological events. This concept article introduces acoustic levitation synthesis as a groundbreaking alternative, uniquely addressing these limitations through a rapid, green, and highly controllable process. By leveraging non-contact acoustic radiation forces, this method enables the synthesis of ultrahigh-density SNAs within minutes under ambient conditions, eliminating the need for toxic reagents or energy-intensive steps. The resulting SNAs exhibit superior homogeneity and stability compared to conventional approaches. We critically evaluate the conceptual novelty and limitations of this technique. Potential applications in surface-enhanced Raman spectroscopy (SERS) and targeted therapeutics are highlighted, positioning acoustic levitation as a transformative tool for next-generation nanobiotechnology.

DNA-programmed nanomaterials: advancing biosensing, bioimaging, and therapeutic applications

DNA-programmed nanomaterials represent a revolutionary convergence of nanotechnology and molecular biology, offering unprecedented precision in the design and application of functional nanostructures. By leveraging the programmability of DNA base-pairing, molecular recognition, and inherent biocompatibility, researchers have developed diverse DNA-engineered nanomaterials for cutting-edge applications in biosensing, bioimaging, and therapeutic delivery. In this review, we systematically explore the construction and functionalization of DNA-conjugated nanomaterials (e.g., DNA-gold nanoparticles, DNA-upconversion nanoparticles, DNA-metal-organic frameworks) and DNA-templated assemblies (e.g., metal nanoclusters, quantum dots), highlighting their tailored physicochemical properties and dynamic responsiveness. Furthermore, we discuss their critical roles in early disease diagnosis, real-time molecular imaging, and precision medicine. By providing a comprehensive overview of recent advancements, this review aims to enhance understanding of the current landscape and inspire future innovations in the controllable assembly and biomedical applications of DNA-programmed nanomaterials.

Cascade-amplification-based electrochemical detection of Akashiwo sanguinea at pre-outbreak stage

Red tide events caused by Akashiwo sanguinea (A. sanguinea) pose a significant threat to ecosystems. However, studies that offer promising approaches for portable and onsite detection with precise identification of A. sanguinea remain insufficient. In this study, we developed an electrochemical biosensor (E-biosensor) for detecting A. sanguinea combined with cascade amplification strategies, termed TDW-E-biosensor. A predictive relationship was also established to predict algal cell density based on electrochemical signals. The experiment results showed that the TDW-E-biosensor was successfully applied for detecting A. sanguinea at the pre-outbreak stage and demonstrated excellent analytical performance, showing a low limit of detection (LOD) of 0.0676 fM and quantitation (LOQ) of 0.102 fM for the three-electrode system, and a low LOD of 6.873 fg μL-1 and LOQ of 20.460 fg μL-1 for the portable system. The accuracy of the TDW-E-biosensor was validated through comparison with droplet digital PCR (ddPCR) and Bland-Altman analysis, demonstrating a high level of agreement (a mean difference of 0.132 and a standard deviation of 0.184). The reliability of the predictive relationship was evidenced by controlled laboratory experiments and Bland-Altman analysis. The developed TDW-E-biosensor provides an innovative and promising tool for early warning efforts regarding harmful algae.

Multiplexed Detection of Tumor Markers and Discrimination of Cancer Cell Types by Laser Ablation-Dielectric Barrier Discharge Ionization-Mass Spectrometry

We present an ambient mass spectrometry immunoassay platform based on specific mass tags detected by laser ablation-dielectric barrier discharge ionization-mass spectrometry (LA-DBDI-MS). It features high sensitivity, multiplexed quantitation, minimal sample consumption, and convenient operation. The organic small-molecule mass tags allow very high sensitivity and quantitative detection of multiple proteins, even of membrane-bound proteins on cell surfaces, through signal amplification (approximately 600 times). By using just 2 μL of serum, we achieved the detection of thrombin (LOD 6.6 pM) and cancer antigen 125 (CA125) (LOD 1.4 U/mL). Seven protein biomarkers, including CA125, carcinoembryonic antigen (CEA), epithelial cell adhesion molecule (EpCAM), protein tyrosine kinase 7 (PTK7), transferrin receptor 1 (CD71), cluster of differentiation 8 alpha protein (CD8a), and cluster of differentiation 33 (CD33), were simultaneously detected in situ in four types of cancer cells within 2 h. This platform is expected to enable multiplexed protein detection in single-drop samples or at the single-cell scale, distinguish different types of cells, and has potential applications in clinical diagnosis.

Biomimetic fluorescence-enhanced platform based on photonic crystals and DNAzyme walker for visualization and quantification of miRNA-21

Developing a fluorescence sensing platform for point-of-care detection of low abundance biomarkers is highly valuable for early diagnosis of disease. Herein, a biomimetic fluorescence-enhanced platform based on photonic crystals and DNAzyme walker was constructed and further applied to visualize and quantify the miRNA-21 in biological samples. The DNAzyme walker was orthogonally activated by the target miRNA-21, which enabled the unlocking of the DNAzyme walker strand and the subsequently repeated substrate cleavage, thus generating enhanced fluorescence signals. Meanwhile, a biomimetic photonic crystals substrate was employed to physically boost the emitted fluorescence signals again, enabling visual detection by naked eyes and quantitative analysis by smartphone. A limit of detection as low as 84.8 pM was obtained and the single base variation in miRNA-21 could also be discriminated. Furthermore, the potential application of this platform was demonstrated in spiked-urine sample and total RNA extracts, showing good agreement with RT-qPCR results. Therefore, the multiple signal amplification strategy-based fluorescent platform has the advantages of high sensitivity, good specificity, good portability and high-throughput analysis, providing a powerful tool for convenient disease diagnosis and health assessment.

OligoA-tailed DNA for dense functionalization of gold nanoparticles and nanorods in minutes without thiol-modification: unlocking cross-disciplinary applications

DNA-functionalized gold nanoparticles (DNA-AuNPs) and nanorods (DNA-AuNRs) have emerged as key yet versatile biomaterials for applications in biosensing, diagnostics and programmable assembly. The high cost and sometimes complex procedures of functionalization of DNA onto AuNPs and AuNRs via the Au-thiol interaction may have set a threshold for its expanded application by researchers of diverse fields. Although oligoA-tailed DNA has been introduced as an alternative to thiolated DNA, its extended use has been largely confined to spherical nanoparticles with suboptimal functionalization density. Here we show a rapid and efficient method for high-density functionalization of both AuNPs and AuNRs using oligoA-tailed DNA via butanol dehydration, with the length of oligoA as short as A2. By preventing secondary structure formation at an elevated temperature, our results demonstrate significantly enhanced DNA adsorption, further allowing for functionalization of a random sequence onto the AuNPs. This yields stable DNA-nanoparticle conjugates with superior stability and durability, suitable for in situ naked-eye loop-mediated isothermal amplification (LAMP) assay of bacterial pathogens and stimuli-responsive self-assembly. This study overcomes long-standing barriers in rapid, simple and low-cost preparation of DNA-AuNPs and DNA-AuNRs, paving the way for cross-disciplinary applications in diverse fields that were previously siloed and beyond.

Robust Peptide-Functionalized Gold Nanoparticles via Ethynyl Bonding for High-Fidelity Bioanalytical Applications

While Au-S bonds have been widely applied in preparing gold nanoparticle (AuNP) bioconjugates for biosensing, cell imaging, and biomedical research, biothiols in complex biological environments can seriously interfere with the stability of the conjugates due to ligand exchange. Herein, we communicate a robust and fast strategy for constructing peptide-functionalized AuNP conjugates (PFCs) using the Au-C≡C bond, which can be completed within two minutes. The resulting Au-C≡C PFCs exhibited better stability and resistance to biothiols than the corresponding Au-S PFCs, and also demonstrated excellent stability in high salt concentration, a wide range of pH values, and varying temperatures. The mechanism of Au-C≡C conjugation was confirmed using molecular dynamics simulation and X-ray photoelectron spectroscopy (XPS). The Au-C≡C PFCs significantly improved the signal fidelity in an intracellular caspase imaging assay. Overall, the developed strategy provides a promising approach for constructing AuNP nanoprobes, allowing reliable detection and broadening the potential for diverse biological applications.

The nucleic acid reactions on the nanomaterials surface for biomedicine

Integrating nucleic acids (NAs) with nanomaterials has substantially advanced biomedical research, enabling critical applications in biosensing, drug delivery, therapeutics, and the synthesis of nanomaterials. At the core of these advances are the reactions of NAs on nanomaterial surfaces, encompassing conjugation (covalent and non-covalent), detachment (physical and chemical), and signal amplification (enzyme-mediated signal amplification, enzyme-free signal amplification, and DNA Walker). Here, we review the fundamental mechanisms and recent progress in nucleic acid reactions on nanomaterial surfaces, discuss emerging applications for diagnostics, nanomedicine, and gene therapy, and explore persistent challenges in the field. We offer a forward-looking perspective on how future developments could better control, optimize, and harness these reactions for transformative advances in nanomedicine and biomedical engineering.

Electron Perturbation for Chiral DNA Point Mutation

Advances in molecular nanotechnology have enabled the design of systems that exploit nanoscale interactions for enhanced biosensing and diagnostics. Here, we present a plasmonic nematic film (PNF) that leverages nanoscale plasmonic hotspots to amplify electron perturbations induced by DNA mutations. Sequence-specific mismatches, particularly point mutations, significantly alter the local electromagnetic environment, leading to distinct and quantifiable spectral shifts in circular dichroism (CD), denoted as Δλdip. These shifts exhibit a strong correlation with target DNA concentration (R2 > 0.99), enabling precise, quantitative detection of mutation-induced asymmetry. The underlying mechanism is modeled by the asymmetric chiral signal Iasy = ∫ΨPNF*(Ω)ΨPNF dV, where ΨPNF is the wave function of the PNF and Ω represents its chiroptical response. Simulations and electric field analysis further validate that mutation-driven perturbations at the PNF-DNA interface enhance local field intensity at λdip, while no significant changes occur at nonresonant wavelengths. Through this mechanism, the PNF platform achieves over 240% enhancement in chiroptical signal compared to wild-type DNA and enables mutation detection down to 1534 pg. These findings highlight the system's potential for high-specificity diagnostics of clinically relevant mutations, including those associated with hereditary hearing impairment, and may inform the development of future chiral biosensing platforms.

Remodeling of Effector and Regulatory T Cells by Capture and Utilization of miRNAs Using Nanocomposite Hydrogel for Tumor-Specific Photothermal Immunotherapy

In immunotherapy for malignant tumors, the dysregulation of the balance between effector T cells and regulatory T cells (Tregs) and the uncertain efficacy due to individual differences have been considered as two critical challenges. In this study, we engineered an injectable nanocomposite hydrogel system (SNAs@M-Gel) capable of suppressing Treg proliferation and blocking PD-1/PD-L1-mediated immune evasion effectively, achieved through the stimulus-responsive modulation of multiple tumor-associated microRNAs. Simultaneously, this system enables microRNA-dependent photothermal immunotherapy, facilitating a highly efficient and personalized approach to tumor treatment. Specifically, oxidized sodium alginate (OSA) and cancer cell membrane (CCM)-encapsulated spherical nucleic acid nanoparticles (SNAs@M) were used to construct the SNAs@M-Gel hydrogel in situ at the tumor site through the formation of pH-sensitive Schiff base bonding and cross-linking using endogenous calcium ions (Ca2+). During treatment, SNAs@M-Gel was retained locally for up to 10 days, and SNAs@M nanoparticles were continuously released into the tumor microenvironment. Through the targeting ability of CCM, SNAs@M precisely entered tumor cells and specifically hybridized with the overexpressed miR-214 and miR-130a, leading to a significant downregulation of PD-L1 expression on tumor cells and the restoration of cytotoxic T lymphocyte (CTL) function suppressed by Tregs, thereby remodeling the immune microenvironment. In addition, miRNAs functioned as cross-linking agents, facilitating the aggregation of SNAs and allowing the localized production of photothermal agents directly inside tumor cells, which, under near-infrared (NIR) irradiation, promoted highly selective photothermal therapy. This cascade of events not only led to the destruction of the primary tumor but also resulted in the release of a substantial number of tumor-related antigens, which triggered the maturation of adjacent dendritic cells (DCs) and subsequent priming of tumor-specific CTLs, while simultaneously depleting Tregs, thereby reversing the tumor-promoting immune microenvironment and enhancing the overall therapeutic efficacy of photothermal immunotherapy.

Effect of Surface Modification of Gold Nanoparticles Loaded with Small Nucleic Acid Sequences on Cytotoxicity and Uptake: A Comparative Study In Vitro

Nanoparticle technology, particularly gold nanoparticles (AuNPs), is being developed for a wide range of applications, including as a delivery system of peptides or nucleic acids (NA). Their use in precision medicine requires detailed engineering of NP functionalization to optimize their function and minimize off-target toxicity. Two main routes can be found in the literature for the attachment of NA strands to AuNPs: covalent binding via a thiol group or passive adsorption onto a specially adapted coating previously applied to the metallic core. In this latter case, the coating is often a positively charged polymer, as polyethylenimine, which due to its high positive charge can induce cytotoxicity. Here, we investigated an innovative strategy based on the initial coating of the particles using calix[4]arene macrocycles bearing polyethylene glycol chains as an interesting alternative to polyethylenimine for NA adsorption. Because any molecular modification of AuNPs may affect the cytotoxicity and cellular uptake, we compared the behavior of these AuNPs to that of particles obtained via a classical thiol covalent attachment in MCF-7 and GC-1 spg cell lines. We showed a high biocompatibility of both AuNPs-NA internalized in vitro. The difference in subcellular localization of both AuNPs-NA in MCF-7 cells compared to GC-1 spg cells suggests that their subcellular target is cell- and coating-dependent. This finding provides valuable insights for developing alternative NA delivery systems with a high degree of tunability.

Functionalization of Nucleic Acid Molecular Machines under Physiological Conditions: A Review

In-situ fabrication of nucleic acid molecular machines in biological environments is desirable for smart theranostic applications. However, given the complex nature of biological environments, the integration of multiple functional modules into a coordinated machine remains challenging. Recent advances in nucleic acid nanotechnology offer solutions to these challenges. Here, we outline design principles for nucleic acid-based molecular machines tailored for physiological conditions, drawing on recent examples. We review cutting-edge technologies that facilitate their functionalization in physiological settings, particularly presynthesis modifications using unnatural bases and postsynthesis functionalization via bioorthogonal chemistry and noncovalent biological interactions. We discuss the advantages and limitations of these technologies and suggest future directions to overcome existing challenges.

Aqueous Two-Phase Submicron Droplets Catalyze DNA Nanostructure Assembly for Confined Fluorescent Biosensing

Membraneless organelles (MLOs) are fundamental to cellular organization, enabling biochemical processes by concentrating biomolecules and regulating reactions within confined environments. While micrometer-scale synthetic droplets are extensively studied as models of MLOs, submicron droplets remain largely unexplored despite their potential to uniquely regulate biomolecular processes. Here, submicron droplets are generated by a polyethylene glycol (PEG)/dextran aqueous two-phase system (ATPS) as a model to investigate their effect on DNA assembly in crowded environments. The findings reveal that submicron droplets exhibit distinct advantages over microdroplets by acting as submicron catalytic centers that concentrate DNA and accelerate assembly kinetics. This enhancement is driven by a cooperative mechanism wherein global crowding from PEG induces an excluded volume effect, while local crowding from dextran provides weak but nonspecific interactions with DNA. By exploiting both the confinement and phase properties of submicron droplets, a rapid and sensitive assay is developed for miRNA detection using confined fluorescent readouts. These findings highlight the unique ability of submicron droplets to amplify biomolecular assembly processes, provide new insights into the interplay between global and local crowding effects in cellular-like environments, and present a platform for biomarker detection and visualization.

A Novel DNA-Platinum Nanoparticle Conjugation Method for Attomolar Detection and Quantitation of Nucleic Acids Using the Microbubbling Digital Assay

Platinum nanoparticles (PtNPs) hold promise for developing novel point-of-care diagnostic tools. This study focuses on the synthesis of single-stranded DNA-platinum nanoparticle (DNA-PtNP) conjugates used as detection probes for nucleic acids in an ultrasensitive and amplification-free microbubbling digital assay. Although significant research exists for synthesizing DNA-gold nanoparticle (AuNP) conjugates, methods for synthesizing stable nucleic acid-PtNP conjugates, especially for larger PtNPs (>50 nm), remain unreported. The instability and slow ligand exchange rate of PtNP colloidal solutions make this synthesis challenging, as conventional methods such as salt aging cause PtNP aggregation and require prolonged durations. This study evaluates the effect of factors such as incubation time, DNA length, salt concentration, pH, and surfactants on DNA loading and hybridization on PtNPs. These findings led to a novel DNA-PtNP conjugation method featuring a 30 min pH-mediated conjugation followed by a 30 min freezing at -20 °C. This conjugation approach is rapid, efficient, and sonication-free, resulting in high DNA loading and hybridization efficiency and stable conjugates. Using these conjugates in the microbubbling digital assay enables the assay to detect and quantify nucleic acids in the attomolar range. Using HCV RNA as an example, the limit of detection of the microbubbling digital assay was 0.68 aM (408 copies/ml or 68 IU/ml). Our findings can be extended to other bio/nano systems, using oligonucleotide-loaded platinum nanoparticles to develop novel molecular diagnostics.

Nucleoside hydrogel-modified cell subtype biosensor with antifouling and electroconductive properties

The point-of-care testing (POCT) of electrochemical biosensors is hindered by biofouling and signal sensitivity. Sometimes the antifouling strategies were used by decreasing the electroconductivity. Addressing the conductivity-antifouling trade-off in electrochemical sensors, we synthesized a novel conductive and antifouling nucleoside hydrogel (C-Ag-C hydrogel). Modified electrodes with this hydrogel exhibited superior recognition of microRNA-21 and microRNA-122, enabling the identification of hepatocellular carcinoma cell subtypes. Utilizing six-channel screen-printed electrodes, we constructed a biosensor with the potential for POCT of cancer cell subtypes.

On-demand reprogramming of immunosuppressive microenvironment in tumor tissue via multi-regulation of carcinogenic microRNAs and RNAs dependent photothermal-immunotherapy using engineered gold nanoparticles for malignant tumor treatment

The frequent immune escape of tumor cells and fluctuating therapeutic efficiency vary with each individual are two critical issues for immunotherapy against malignant tumor. Herein, we fabricated an intelligent core-shell nanoparticle (SNAs@CCMR) to significantly inhibit the PD-1/PD-L1 mediated immune escape by on-demand regulation of various oncogenic microRNAs and perform RNAs dependent photothermal-immunotherapy to achieve precise and efficient treatment meeting the individual requirements of specific patients by in situ generation of customized tumor-associated antigens. The SNAs@CCMR consisted of antisense oligonucleotides grafted gold nanoparticles (SNAs) as core and TLR7 agonist imiquimod (R837) functionalized cancer cell membrane (CCM) as shell, in which the acid-labile Schiff base bond was used to connect the R837 and CCM. During therapy, the acid environment of tumor tissue cleaved the Schiff base to generate free R837 and SNAs@CCM. The SNAs@CCM further entered tumor cells via CCM mediated internalization, and then specifically hybridized with over-expressed miR-130a and miR-21, resulting in effective inhibition of the migration and PD-L1 expression of tumor cells to avoid their immune escape. Meanwhile, the RNAs capture also caused significant aggregation of SNAs, which immediately generated photothermal agents within tumor cells to perform highly selective photothermal therapy under NIR irradiation. These chain processes not only damaged the primary tumor, but also produced plenty of tumor-associated antigens, which matured the surrounding dendritic cells (DCs) and activated anti-tumor T cells along with the released R837, resulting in the enhanced immunotherapy with suppressive immune escape. Both in vivo and in vitro experiments demonstrated that our nanoparticles were able to inhibit primary tumor and its metastasis via multi-regulation of carcinogenic microRNAs and RNAs dependent photothermal-immune activations, which provided a promising strategy to reprogram the immunosuppressive microenvironment in tumor tissue for better malignant tumor therapy.

Recent advances in nucleic acid-functionalized metallic nanoparticles

Nucleic acid-functionalized metallic nanoparticles (N-MNPs) precisely integrate the advantageous characteristics of nucleic acids and metallic nanomaterials, offering various abilities such as resistance to enzymatic degradation, penetration of physiological barriers, controllable mobility, biomolecular recognition, programmable self-assembly, and dynamic structure-function transformation. These properties demonstrate significant potential in the field of biomedical diagnostics and therapeutics. In this review, we examine recent advancements in the construction and theranostic applications of N-MNPs. We briefly summarize the methodologies employed in the conjugation of nucleic acids with metallic nanoparticles and the formation of their superstructural assemblies. We highlight recent representative applications of N-MNPs in biomolecular diagnosis, imaging, and smart delivery of theranostic agents. We also discuss challenges currently faced in this field and provide an outlook on future development directions and application prospects.

DNA-Engineered Coating for Protecting the Catalytic Activity of Platinum Nanozymes in Biological Systems

Nanozymes, exemplified by metal nanoparticles, have shown promise in the fields of biological diagnostics and therapeutics. However, their practical application is often hindered by aggregation or deactivation in complex biological systems. Here, we develop a DNA-engineered nanozyme coating to preserve the peroxidase-like catalytic activity of platinum nanoparticles in complex biological environments. We employed thiol-modified single-stranded DNA to coat the platinum nanoparticles through metal-sulfur interaction. We found that the negatively charged DNA coating prevents the aggregation of platinum nanoparticles in high-salt environments. Moreover, the DNA coating functions as a molecular sieve, inhibiting non-specific protein adsorption while preserving substrate access to the catalytic interface, thus sustaining high peroxidase-like catalytic activity in serum. As a proof of concept, we demonstrate miRNA detection in serum samples with a detection limit of 1 fM. This approach offers a versatile strategy for molecular diagnostics of nanozymes in complex biological environments.

DNA‑Directed Assembly of Photonic Nanomaterials for Diagnostic and Therapeutic Applications

DNA-directed assembly has emerged as a versatile and powerful approach for constructing complex structured materials. By leveraging the programmability of DNA nanotechnology, highly organized photonic systems can be developed to optimize light-matter interactions for improved diagnostics and therapeutic outcomes. These systems enable precise spatial arrangement of photonic components, minimizing material usage, and simplifying fabrication processes. DNA nanostructures, such as DNA origami, provide a robust platform for building multifunctional photonic devices with tailored optical properties. This review highlights recent progress in DNA-directed assembly of photonic nanomaterials, focusing on their applications in diagnostics and therapeutics. It provides an overview of the latest advancements in the field, discussing the principles of DNA-directed assembly, strategies for functionalizing photonic building blocks, innovations in assembly design, and the resulting optical effects that drive these developments. The review also explores how these photonic architectures contribute to diagnostic and therapeutic applications, emphasizing their potential to create efficient and effective photonic systems tailored to specific healthcare needs.

Density and structure of DNA immobilised on gold nanoparticles affect sensitivity in nucleic acid detection

Gold nanoparticles (AuNPs) are used as colorimetric biosensors that, combined with immobilised single-stranded DNA (ssDNA-AuNPs), can be used in genetic diagnosis because of their rapid and sequence-specific aggregation properties. Herein, we investigated the effect of the steric structure and density of immobilised DNA on AuNPs in non-crosslinking aggregation-based nucleic acid detection. Detection sensitivity improved with decreasing DNA density for linear conformations, but worsened for those with more rigid stem structures. We controlled the density of immobilised DNA using two different methods and investigated the aggregation behaviour of ssDNA-AuNPs. Interestingly, controlling the immobilised DNA density through ethylene glycol treatment had different effects on ssDNA-AuNP aggregation compared to those of alkanethiol substitution. This study suggests that the sensitivity of ssDNA-AuNPs for detecting target DNA could be affected by density and structure of the immobilised DNA.

A ratiometric electrochemical aptasensor for Ochratoxin A detection based on electroactive Cu-MOF and DNA conjugates resembling the structure of Bidens pilosa

BACKGROUND

Ochratoxin A (OTA) represents a naturally occurring mycotoxin with a serious hazard to the health of individuals because of carcinogenic and teratogenic properties. To date, various analytical methods have been developed for the detection of OTA, among which aptamer-based electrochemical sensing has attracted significant attention due to its rapidity and high sensitivity. As a subtype of aptamer-based electrochemical sensing, ratiometric electrochemical methods further exhibit excellent anti-interference capability. However, their analytical performance remains limited by the labor-intensive and resource-consuming modification of electroactive signal molecules, as well as the restricted specific surface area of the electrodes.

RESULT

Here, we develop a ratiometric electrochemical aptasensor functionalized with Bidens pilosa-like DNA-gold structures and copper-based metal-organic frameworks (Cu-MOFs) for OTA detection. Cu-MOFs served as a substrate for electrode modification, performing two key roles: 1) providing a large surface area for aptamer immobilization, and 2) generating one current signal. Double-stranded DNA-gold nanoparticles (dsDNA-AuNPs) were assembled through Au-S bonding. The dsDNA-AuNPs conjugates, structurally resembling Bidens pilosa, could load more dsDNA and connect to Cu-MOFs via π-π stacking. When OTA was present, the aptamer-OTA complex was stripped from the aptasensor, reducing the amount of Fc-Apt, thus decreasing the corresponding Fc current (IFc). Simultaneously, the decreased interfacial resistance caused an increase in the Cu-MOF current (ICu), providing the decreased IFc/ICu ratio as a quantitative indicator. The aptasensor exhibited a linear detection range from 0.01 ng mL-1 to 300 ng mL-1, with a detection limit of 0.002 ng mL-1 for OTA.

SIGNIFICANCE

The developed electrochemical ratiometric aptasensor demonstrated high reproducibility and stability, and it was successfully applied to maize sample analysis, underscoring its practical applicability. Moreover, it provides a promising strategy for the application of Cu-MOF-based electrochemical aptasensors. Furthermore, the modification procedures of the developed aptasensor were simplified by preparing dsDNA-AuNPs in solution rather than assembling them step-by-step on the electrode surface.

Freeze-Thaw Imaging for Microorganism Classification Assisted with Artificial Intelligence

Fast and cost-effective microbial classification is crucial for clinical diagnosis, environmental monitoring, and food safety. However, traditional methods encounter challenges including intricate procedures, skilled personnel needs, and sophisticated instrumentations. Here, we propose a cost-effective microbe classification system, also termed freeze-thaw-induced floating pattern of AuNPs (FTFPA), coupled with artificial intelligence, which is capable of identifying microbes at a cost of $0.0023 per sample. Specifically, FTFPA utilizes AuNPs for coincubation with microbes, resulting in distinct patterns upon freeze-thawing due to their weak interaction. These patterns are digitized to train models that distinguish nine microbes in various tasks. The positive sample detection model achieved an F1 score of 0.976 (n = 194), while the multispecies classification task reached a macro F1 score of 0.859 (n = 1728). To address scalability and lightweight requirements across diverse classification scenarios, we categorized microbes based on species classification levels. The macro F1 score of the hierarchical model (n = 5184), order level model (n = 5184), Enterobacteriales level model (n = 2550), and Bacillales level model (n = 1974) was 0.854, 0.907, 0.958, and 0.843. In summary, our method is user-friendly, requiring only simple equipment, is easy to operate, and convenient, providing a platform for microbial identification.

Applications of DNA functionalized gold nanozymes in biosensing

In recent years, nanozymes have emerged as highly potential substitutes, surpassing the performance of natural enzymes. Among them, gold nanoparticles (AuNPs) and their metal hybrids have become a hot topic in nanozyme research due to their facile synthesis, easy surface modification, high stability, and excellent enzymatic activity. The integration of DNA with AuNPs, by precisely controlling the assembly, arrangement, and functionalization of nanoparticles, greatly facilitates the development of highly sensitive and selective biosensors. This review comprehensively elaborates on three core strategies for the combination of DNA with AuNPs, and deeply analyzes two widely applied enzyme activities in the field of sensing technology and the catalytic principles behind them. On this basis, we systematically summarize various methods for regulating the activity of gold nanozymes by DNA. Following that, we comprehensively review the latest research trends of DNA-Au nanozymes in the field of biosensing, with a particular focus on several crucial application areas such as food safety, environmental monitoring, and disease diagnosis. In the conclusion of the article, we not only discuss the main challenges faced in current research but also look forward to potential future research directions.

Dual Protein Corona-Mediated Target Recognition System for Visual Detection and Single-Molecule Counting of Nucleic Acids

Rapid, highly sensitive, and specific nucleic acid detection plays a crucial role in advancing point-of-care (POC) diagnostics for pathogens and viruses, cancer monitoring, and optimizing clinical treatments. Herein, leveraging the precise recognition ability of CRISPR/dCas9 and the powerful localized surface plasmon resonance (LSPR) of gold nanoparticles (AuNPs), we report the design of a dual protein corona-mediated detection platform to simultaneously fulfill rapid POC testing and single-molecule counting of nucleic acids in a one-pot and one-step manner. This system uses guide RNA as a molecular bridge to anchor dCas9 protein onto AuNPs, forming artificial protein coronas. Upon recognizing a target, the interaction between the two protein coronas on the same nucleic acid molecule triggers cross-linked aggregation of AuNPs. Then, a target as low as 100 aM can be visually detected within 30 min, making the platform particularly well-suited for rapid POC application and the screening of emerging epidemics. Additionally, the superior LSPR properties of AuNPs increase the light-scattering signal generated during target-induced aggregation, enabling the visualization of the aggregated AuNPs as diffraction-limited spots under confocal microscopy. By counting these spots, the platform achieves unprecedented detection sensitivity, identifying a target as low as 1 aM, which is equivalent to just 6 molecules in a 10 μL system, demonstrating single-molecule detection capability. This dual protein corona-mediated detection system offers exceptional promise for large-scale screening of pathogenic viruses and the early detection of cancer, particularly in applications requiring ultrahigh sensitivity at the single-molecule level.

Effect of DNA Density on Nucleic Acid Detection Using Cross-Linking Aggregation of DNA-Modified Gold Nanoparticles

Gold nanoparticles (AuNPs) have been utilized as colorimetric biosensors by which target molecule-induced AuNP aggregation is recognized by a color change from red to blue. Particularly, single-stranded DNA (ssDNA)-immobilized AuNPs (ssDNA-AuNPs) have been applied to genetic diagnosis. Herein, we investigated the effect of the density of immobilized ssDNA on the sensitivity of the target ssDNA detection using two different cross-linking aggregation models of ssDNA-AuNPs, i.e., the unidirectional (UD) type and bidirectional (BD) type. We demonstrated that target ssDNA detection was more sensitive in both types of aggregation models when smaller amounts of immobilized ssDNA were used. Interestingly, the UD type was more sensitive in detecting the target than the BD type possibly due to the number of cross-links. It was also shown that the sensitivity differed depending upon the number of bases between the AuNPs at higher DNA density. Our results indicate that control of immobilized probe ssDNA density improves the detection sensitivity and duplex formation ratio in cross-linking aggregation.

Surface-Engineered Nanoparticles Enhance the Peroxidase Activity of Heme-Containing Proteins

Enzymes interfaced with nanomaterials often lose more than 90% of their activity; yet, some nanomaterials have been shown to enhance enzyme activity. However, these findings are largely observational and lack clear and actionable design principles. Systematic studies are needed to develop nanomaterials that can control and tune enzyme activity. Given that enzyme-nanomaterial interactions are mediated by their surface functional groups, we hypothesized that engineering nanoparticle surfaces could allow for controlled tuning of the enzyme activity. In this study, we used peptide-functionalized gold nanoparticles (PGNPs) as a programmable platform to investigate how surface functionalization affects enzyme activity. By varying the peptide sequences, we examined the effects of charge, hydrophobicity, peptide length, and structure on the peroxidase activity of cytochrome C (Cyt C). Our results showed that carefully designed ligands can significantly enhance enzyme activity, exceeding 10-fold compared with the free enzyme. Molecular dynamics simulations provided insights into the molecular basis of these findings, revealing the preferred orientation of Cyt C upon adsorption and key interaction patterns between the enzyme and peptide ligands, thus bridging experimental results with a mechanistic understanding. Furthermore, PGNPs proved to be a versatile platform for boosting peroxidase activity of other heme-containing proteins such as lactoperoxidase, hemoglobin, and catalase by 13.4-, 3.9-, and 4.2-fold, respectively. This study highlights the potential of nanoparticle surface engineering to activate enzymes at interfaces in a tunable manner, offering a promising alternative to protein engineering for developing biocatalysts.

N-Doped Porous Carbon Synergistic Freezing-Induced DNA with Catalyzed Hairpin Assembly Enables Electrochemical One-Pot Detection of Pathogen in Food Samples

A DNA electrochemical interface biosensor based on screen-printed carbon electrodes (SPCEs) holds promise for point-of-care testing (POCT) detection of pathogens in food safety. Nevertheless, SPCE commonly has a rough surface and suffers from a relatively low electron transfer rate, disorder of DNA capture probes (CPs), and the steric hindrance effect of target nucleic acid binding. These issues lead to a low sensitivity. Herein, a simple and rapid electrochemical biosensor based on N-doped porous carbon (NPC)-modified SPCE and freezing-directed DNA combined with catalyzed hairpin assembly (CHA) was constructed for the one-pot detection of pathogens in food samples without time-consuming growth cultures. The biosensor was constructed by SPCE modified with NPC for enhanced electrochemical properties, and the DNA CP designed for CHA was stably fixed on the electrode for a high hybridization efficiency. Moreover, the signals amplified by CHA enable the selective and sensitive detection of pathogens without washing steps. This one-pot method is simple and sensitive with a wide detection linear range of 101 to 107 CFU/mL and limit of detection of 5 CFU/mL for Escherichia coli and shows specificity against other coexisting pathogens. The whole detection of pathogens in complex samples is performed only within 60 min from sample-to-answer, which has great potential for POCT of pathogens in food safety.

Antiprotein Corona-Fouling Effect of the Double-Stranded DNA Coating Layer on the Gold Nanoparticles-Small Molecule Adsorbent Probe

The formation of a protein corona (PC) can significantly impact the detection ability of gold nanoparticles (AuNPs)-small molecule adsorbent probes based on competitive adsorption. To alleviate this problem, in this study, double-stranded DNA (dsDNA) was introduced to modify the AuNP probes to mitigate the negative effect of PCs on the detection of small molecules by taking the AuNPs-dichlorofluorescein (DCF) probe-based detection of ambroxol hydrochloride (AMB) as a study model. It was found that based on the dsDNA-modified AuNPs-DCF probe (dsDNA@AuNPs-DCF), the accuracy for the detection of AMB was significantly improved, which might be attributed to the isolation of proteins from the surface of AuNPs while still allowing small molecules to access the surface due to the introduction of rigid dsDNA. Further, the effect of the strand length and the number of dsDNA modified on the surface of AuNPs on the antifouling performance was then investigated, and it was found that the LOD value of AMB in artificial milk samples by dsDNA10bp90@AuNPs-DCF probes (with 10 base strand length and 90:1 ratio of dsDNA to AuNPs) is decreased more than 2-fold compared with that by the AuNPs-DCF probe. Moreover, based on dsDNA10bp90@AuNPs-DCF probes, the recovery rates of AMB analyzed in commercial milk samples greatly improved compared with that with the AuNPs-DCF probe, particularly when the samples contained AMB with much lower concentrations. This study demonstrates a dsDNA-based antiprotein corona-fouling strategy for the AuNPs-small molecule adsorbent probe, which provides beneficial ideas for dealing with the interference resulting from PCs to the studying of biological samples.

Advanced Synthesis of Spherical Nucleic Acids: A Limit-Pursuing Game with Broad Implications

Spherical nucleic acids (SNAs) consist of DNA strands arranged radially and packed densely on the surface of nanoparticles. Due to their unique properties, which are not found in naturally occurring linear or circular DNA, SNAs have gained widespread attention in fields such as sensing, nanomedicine, and colloidal assembly. The rapidly evolving applications of SNAs have driven a modernization of their syntheses to meet different needs. Recently, several advanced approaches have emerged, enabling ultrafast, quantitative, and low-cost SNA synthesis with maximal DNA grafting through "counterintuitive" processes like freezing and dehydration. This concept paper discusses these critical developments from a synthetic perspective, focusing on their underlying mechanisms and broad implications, with a goal of inspiring future research in related fields.

An enzyme-free immunosorbent assay of staphylococcal enterotoxin B using a three-way DNA junction amplifier with an automatic reset function

A highly sensitive immunoadsorption assay without traditional horseradish peroxidase for signal amplification was developed, utilizing a three-way DNA junction amplifier instead. The formation of a three-way DNA junction and release of trigger DNA with recycling was accomplished by toehold-mediated strand displacement. The fluorescent dye N-methyl mesoporphyrin IX, with highly structure-specific binding affinity towards G-quadruplexes, was employed for label-free and simple signal output. High sensitivity was achieved for concentrations as low as 7.21 pg mL-1 by targeting Staphylococcal enterotoxin B for detection, and its applicability was confirmed by a recovery study of precooked dishes.

Quaternized and boronic acid dual-functional CoAg nanozymes for label-free, stable, sensitive, and rapid quantitation detection of the bacterial total concentration

BACKGROUND

Foodborne pathogenic bacteria lead to a significant increase in illnesses and fatalities annually. In the early stage of a pathogenic bacterial infection, the concentration of bacteria in food is lower than the detection limit of most technology which enhances the difficulty in diagnosis. It is a serious challenge for researchers to develop a rapid, sensitive, accurate, and stable pathogenic bacterial determination method without costly equipment and highly skilled operators.

RESULTS

It is clear that the bacterial total concentration in food increased obviously could be attributed to microbial contamination in food. Herein, quaternized and boronic acid dual-functional capped CoAg nanozymes, known as CoAg@HTCC-B, were developed and synthesized to exhibit strong and stable chemiluminescence (CL) emission to detect bacterial total concentrations. The CoAg@HTCC-B nanozymes are capable of accurately quantifying the total concentrations of a mixed bacterial solution (S. aureus and E. coli) over a broad detection range and with a low limit of detection (LOD). These nanozymes were utilized for the detection of E. coli or S. aureus in fresh chicken samples with LOD values of 2.08 colony-forming units per milliliter (CFU/mL) for E. coli and 1.71 CFU/mL for S. aureus.

SIGNIFICANCE

This suggests that the CoAg@HTCC-B nanozymes have the potential for early-stage monitoring of microbial contamination in meat samples. The capability of CoAg@HTCC-B nanozymes in swiftly and accurately detecting known bacterial concentrations suggested their potential as a viable alternative to the traditional culture-based approach for quantitatively determining known bacterial concentrations in academic, research, or industrial settings.

Spatioselective Imaging of Noncoding RNAs in Mitochondria via an Organelle-Specific DNA Assembly Strategy

Precise imaging of noncoding RNAs (ncRNAs) in specific organelles allows decoding of their functions at subcellular level but lacks advanced tools. Here we present a DNA-based nanobiotechnology for spatially selective imaging of ncRNA (e.g., microRNA (miRNA)) in mitochondria via an organelle-specific DNA assembly strategy. The target miRNA-initiated assembly of DNA hairpins is inhibited by the block of toehold-mediated strand displacement reaction but can be exclusively activated by a mitochondria-encoded ribosomal RNA (rRNA) for hybridization chain reaction, enabling spatial control over miRNA imaging. We demonstrate that the conditionally controlled DNA assembly technology allows for minimization of nonspecific activation and thus improves the spatial precision of miRNA detection. In addition, the strategy is adaptable to visualizing other ncRNAs such as long noncoding RNAs in mitochondria, highlighting the universality of the approach. Overall, this work provides a useful tool for spatially selective imaging of ncRNAs and investigating the functions of organelle-located RNA.

Label-free (fluorescence-free) sensing of a single DNA molecule on DNA origami using a plasmon-enhanced WGM sensor

The integration of DNA origami structures with opto-plasmonic whispering gallery mode (WGM) sensors offers a significant advancement in label-free biosensing, overcoming the limitations of traditional fluorescence-based techniques, and providing enhanced sensitivity and specificity for detecting DNA hybridization events. In this study, DNA origami acts as a scaffold for the precise assembly of plasmonic dimers, composed of gold nanorods (AuNRs), which amplify detection sensitivity by generating strong near-field enhancements in the nanogap between the nanorods. By leveraging the strong electromagnetic fields generated within the nanogap of the plasmonic dimer, this platform enables the detection of transient hybridization events between DNA docking strands and freely diffusing complementary sequences. Our findings demonstrate that the salt concentration critically influences DNA hybridization kinetics. Higher ionic strengths reduce electrostatic repulsion between negatively charged DNA strands, thereby stabilizing duplex formation and prolonging interaction times. These effects are most pronounced at salt concentrations around 300-500 mM, where optimal conditions for duplex stability and reduced dissociation rates are achieved. By thoroughly investigating the hybridization kinetics under varying environmental conditions, this study contributes to a deeper understanding of DNA interactions and offers a robust tool for single-molecule detection with real-time capabilities.

Giant Purcell Broadening and Lamb Shift for DNA-Assembled Near-Infrared Quantum Emitters

Controlling the light emitted by individual molecules is instrumental to a number of advanced nanotechnologies ranging from super-resolution bioimaging and molecular sensing to quantum nanophotonics. Molecular emission can be tailored by modifying the local photonic environment, for example, by precisely placing a single molecule inside a plasmonic nanocavity with the help of DNA origami. Here, using this scalable approach, we show that commercial fluorophores may experience giant Purcell factors and Lamb shifts, reaching values on par with those recently reported in scanning tip experiments. Engineering of plasmonic modes enables cavity-mediated fluorescence far detuned from the zero-phonon-line (ZPL)─at detunings that are up to 2 orders of magnitude larger than the fluorescence line width of the bare emitter and reach into the near-infrared. Our results point toward a regime where the emission line width can become dominated by the excited-state lifetime, as required for indistinguishable photon emission, bearing relevance to the development of nanoscale, ultrafast quantum light sources and to the quest toward single-molecule cavity QED. In the future, this approach may also allow the design of efficient quantum emitters at infrared wavelengths, where standard organic sources have a reduced performance.

Simultaneous or separate detection of heavy metal ions Hg2+ and Ag+ based on lateral flow assays

A lateral flow assay (LFA) was developed for the simultaneous or separate detection of mercury ion and silver ion based on isothermal nucleic acid amplification. T-Hg2+-T and C-Ag+-C were utilized in the isothermal nucleic acid amplification strategy to form specific complementary base pairs. Under the action of KF polymerase and endonuclease Nt.BbvCl, trace amounts of Hg2+ and Ag+ were converted to Product-Hg2+ and Product-Ag+ as bridges. Biotin-labeled capture strands (Biotin-DNA1, Biotin-DNA1, and Biotin-DNA3) immobilized on the test strips could capture the Au NPs-DNA nanoprobes by hybridization with the generated bridge products for monitoring of two heavy metal ions simultaneously or separately. The assembly method of DNAs on the nanoprobes was explored, and the DNA sequences on the nanoprobes were designed so that only one kind of DNA strand was used to bind to all three capture DNA strands on the C, T1, and T2 bands. Under optimal detection conditions, the limits of detection for Hg2+ and Ag+ were 2.19 and 5.41 pM, respectively, with desired selectivity and reproducibility.

Amplification-free sensitive detection of Staphylococcus aureus by spherical nucleic acid triggered CRISPR/Cas12a and Poly T-Cu reporter

A spherical nucleic acid (SNA, AuNPs-aptamer) into CRISPR/Cas12a system combined with poly T-template copper nanoparticles as fluorescence reporter was fabricated to establish an amplification-free sensitive method for Staphylococcus aureus (S. aureus) detection. This method, named PTCas12a, utilizes the concept that the bifunction of SNA recognizes the S. aureus and triggers the Cas12a cleavage activity. Then, the Cas12a enzyme cleaves the Poly T40 to generate a signal change in Poly T-Cu fluorescence, indicating the presence or absence of the target bacteria. The PTCas12a platform demonstrated a detection limit as low as 3.0 CFU/mL (3 N/S) in a wide response range of 1.0 × 101-1.0 × 106 CFU/mL for S. aureus detection, which holds significant potential in ensuring food safety and preventing the spread of diseases.

Freeze-Thaw-Induced Patterning of Extracellular Vesicles with Artificial Intelligence for Breast Cancers Identifications

Extracellular vesicles (EVs) play a crucial role in the occurrence and progression of cancer. The efficient isolation and analysis of EVs for early cancer diagnosis and prognosis have gained significant attention. In this study, for the first time, a rapid and visually detectable method termed freeze-thaw-induced floating patterns of gold nanoparticles (FTFPA) is proposed, which surpasses current state-of-the-art technologies by achieving a 100 fold improvement in the limit of detection of EVs. Notably, it allows for multi-dimensional visualizations of EVs through site-specific oligonucleotide incorporation. This capability empowers FTFPA to accurately identify EVs derived from subtypes of breast cancers with artificial intelligence algorithms. Intriguingly, learning the freezing-thawing-microstructures of EVs with a random forest algorithm is not only able to distinguish their original cell lines (with an accuracy of 95.56%), but also succeed in processing clinical samples (n = 156) to identify EVs by their healthy donors, breast lump and breast cancer subtypes (Luminal A, Triple-negative breast cancer, and Luminal B) with an accuracy of 83.33%. Therefore, this AI-empowered micro-visualization method establishes a rapid and precise point-of-care platform that is applicable to both fundamental research and clinical settings.

Development of aptamer-based lateral flow devices for rapid detection of SARS-CoV-2 S protein and uncertainty assessment

The outbreak and spread of COVID-19 have highlighted the urgent need for early diagnosis of SARS-CoV-2. Nucleic acid testing as an authoritative tool, is cumbersome, time-consuming, and easy to cross-infect, while the available antibody self-testing kits are deficient in sensitivity and stability. In this study, we developed competitive aptamer-based lateral flow devices (Apt-LFDs) for the quantitative detection of SARS-CoV-2 spike (S) protein. Molecular docking simulation was used to analyze the active binding sites of the aptamer to S protein, guiding complementary DNA (cDNA) design. Then a highly efficient freezing strategy was applied for the conjugation of gold nanoparticles (AuNPs) and DNA probes. Under optimal conditions, the linear range of the constructed Apt-LFDs was 0.1-1 μg/mL, and the limit of detection (LOD) was 51.81 ng/mL. The cross-reactivity test and stability test of the Apt-LFDs showed good specificity and reliability. The Apt-LFDs had recoveries ranging from 89.45 % to 117.12 % in pharyngeal swabs. Notably, the uncertainty of the analytical result was evaluated using a "bottom-up" approach. At a 95 % confidence level, the uncertainty report of (453.37±54.86) ng/mL with k = 2 was yielded. Overall, this study provides an important reference for the convenient and reliable detection of virus proteins based on LFDs.

Excellent properties of NaF and NaBr induced DNA/gold nanoparticle conjugation system: Better stability, shorter modified time, and higher loading capacity

The functionalization of gold nanoparticle (AuNP) is the key procedure for the biochemical and biomedical application. The conventional salt-aging method requires the stepwise additions of NaCl and excessive thiolated DNA, mainly due to the poor tolerance of the DNA/AuNP mixture toward NaCl. Herein, we found that NaF is capable of improving the stability for the modification of AuNP with different bases of DNA sequences (poly A/T/C/G), and allows for adding up with a high concentration of 200 mM at one time, which greatly reduces the total modification time to 0.5-1 h. Intriguingly, the introduction of NaBr effectively increases the DNA loading capacity. Besides the advantages of NaF and NaBr, the modification performance is improved via the introduction of the oligo A/T spacer for the G-rich DNA sequences. Furthermore, this method shows the superiority to another two methods (pH 3-based and salt-aging) in terms of the loading capacity or sequence components.

Bioinspired Spatial Compartment of Substrate Molecules and Catalytic Counting Entities in Hierarchical MOFs Initiated for a Dual-Mode Glycoprotein Assay

Living cell systems possess multiple isolated compartments that can spatially confine complex substances and shield them from each other to allow for feedback reactions. In this work, a bioinspired design of metal-organic frameworks (MOFs) with well-defined multishelled matrices was fabricated as a hierarchical host for multiple guest substances including fluorogenic molecules and catalytic nanoparticles (NPs) at the separated locations for the development of a dual-mode glycoprotein assay. The multispatial-compartmental zeolitic imidazolate framework-8 (ZIF-8) constituents were synthesized via epitaxial shell-by-shell overgrowth to guide the integration and spatial organization of host guests. The specific property toward glycoprotein recognition was guaranteed by both the antibody-antigen recognition and covalent bonding through boronate-glycan affinity, and the immediate signal responses were initiated by textural collapse of the ZIF-8 integrity. In addition, the inner micropore and the enclosed space of ZIF-8 can avoid the surpassed contact between molecular substances and catalytic entities, inherently. Furthermore, multishelled ZIF-8 can function as a hierarchical matrix for hosting abundant fluorogenic substrates and a large number of catalytic Pt-shelled Au (AuPt) NPs, which can signify its signal amplification means, while upon the stimuli-responsive framework collapse, the signal generators can be harvested in the on-demand manner. Besides, endowing Pt shells on inert plasmonic NPs can not only mimic peroxidase-like catalytic behavior involved in a fluorogenic catalytic reaction to generate fluorescence signals but also function as scattering signal reporters, which can also signify the dynamic light scattering output signals. Collectively, our proposed method may provide a new thought in combining the well-defined multishelled MOF matrices for dual-signal generators in a stimuli-responsive manner, which can also reinforce the accurate detection capability for the glycoprotein assay.

Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence

Multivalency as an interaction principle is widely utilized in nature. It enables specific and strong binding by multiple weak interactions through enhanced avidity and is a core process in immune recognition and cellular signaling, which is also a current concept in drug design. Here, we use the high signals from plasmon-enhanced fluorescence of nanoparticles to extract binding kinetics and dynamics of multivalent interactions on the single-molecule level and in real time. We study mono-, bi-, and trivalent binding interactions using a DNA Holliday Junction as a model construct with programmable valency and introduce a step-binding model for binding kinetics relevant for structured macromolecules by including an experimentally extractable binding restriction term ω to quantify the effects from conformation, steric effects, and rigidity. We used this approach to explore how length and flexibility of the DNA ligands affect binding restriction and binding strength, where the overall binding strength decreased with spacer length. For trivalent systems, increasing spacer length additionally activated binding in the trivalent state, giving insight into the design of multivalent drug or targeting moieties. By systematically changing the receptor density, we explored the binding super selectivity of the multivalent HJ at the single-molecule level. We find a polynomial behavior of the trivalent binding strength that clearly shows receptor-density-dependent selective binding. Interestingly, we could exploit the rapidly decaying near fields of the plasmon that induce a strong dependence of the signal on the position of the dye to observe binding dynamics during single multivalent binding events.

Freezing Functional Nucleic Acids: From Molecular Reactions to Surface Immobilization

Biochemical reactions are typically slowed down by decreasing temperature. However, accelerated reaction kinetics have been observed for a long time. More recent examples have highlighted the unique role of freezing in fabricating supermaterials, degrading environmental contaminants, and accelerating bioreactions. Functional nucleic acids are DNA or RNA oligonucleotides with versatile properties, including target recognition, catalysis, and molecular co4mputing. In this review, we discuss the current observations and understanding of freezing-facilitated reactions involving functional nucleic acids. Molecular reactions such as ligation/conjugation, cleavage, and hybridization are discussed. Moreover, freezing-induced DNA-nanoparticle conjugations are introduced. Then, we describe our effect in immobilizing DNA on bulk surfaces. Finally, we address some critical questions and research opportunities in the field.

Rapid Thermal Drying Synthesis of Nonthiolated Spherical Nucleic Acids with Stability Rivaling Thiolated DNA

Attaching DNA oligonucleotides to gold nanoparticles (AuNPs) to prepare spherical nucleic acids (SNAs) has offered tremendous insights into surface chemistry with resulting bioconjugates serving as critical reagents in biosensors and nanotechnology. While thiolated DNA is generally required to achieve stable conjugates, we herein communicate that using a thermal drying method, a high DNA density and excellent SNA stability was achieved using nonthiolated DNA, rivaling the performance of thiolated DNA such as surviving 1 M NaCl, 2 month stability in 0.3 M NaCl and working in 50 % serum. A poly-adenine block with as few as two consecutive terminal adenine bases is sufficient for anchoring on AuNPs. By side-by-side comparison with the salt-aging method, the conjugation mechanism was attributed to competitive adenine adsorption at high temperature along with an extremely high DNA concentration upon drying. Bioanalytical applications of nonthiolated SNAs were validated in both solution and paper-based sensor platforms, facilitating cost-effective applications for SNAs.