Highly Uniform DNA Monolayers Generated by Freezing-Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood

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.

Solution-phase nucleic acid reaction weaves interfacial barriers on unmodified electrodes: Just-in-time generation of sensor interface for convenient and highly sensitive bioassays

Electrochemical bioassays that rely on sensor interfaces based on immobilized DNA probes often encounter challenges such as complex fabrication processes and limited binding efficiency. In this study, we developed a novel electrochemical bioassay that bypasses the need for probe immobilization by employing a solution-phase nucleic acid reaction to create interfacial barriers on unmodified electrodes, enabling rapid, just-in-time sensor interface formation. Specifically, a 3'-phosphorylated recognition probe was used to identify the target microRNA-21 (miR-21), followed by target recycling facilitated by duplex-specific nuclease (DSN), which resulted in extensive hydrolysis of the recognition probe into DNA fragments with 3'-hydroxyl ends. These fragments were then extended by terminal deoxynucleotidyl transferase (TdT) to form long poly(A) tails. The extended products hybridized with a thiolated assembly probe rich in thymine bases and subsequently assembled on the unmodified gold electrode (AuE) surface, creating a "barrier effect" that hindered the adsorption of streptavidin-HRP (SA-HRP) on the AuE, generating a detectable electrochemical signal. This method demonstrated excellent analytical performance, with a linear detection range from 10 fM to 10 nM and a detection limit as low as 4.3 fM. Moreover, the assay was successfully applied to detect miR-21 in real biological samples, including cell lines and bladder urothelial carcinoma surgical resection specimens, showing strong concordance with RT-qPCR results. The developed method offers a new approach for establishing electrochemical bioassays without the need for pre-immobilization of probes and with minimal reagent use, presenting a promising tool for clinical diagnostics and cancer research.

A DNA Tetrahedron Assembly-Based Nanoshell-Mediated Nanoflares for Intracellular MiRNA Imaging: Reducing False Positivity and Improving Reaction Kinetics and Efficiency

Nanoflares (NFs) are extensively used for the analysis of biomarkers within living cells. However, the severe false positives and low reaction efficiency and kinetics have restricted the further application of NF. To address these issues, we have developed an aptamer-modified DNA tetrahedron-assembled 3D nucleic acid nanoshell-mediated nanoflares (Ap-TDN-NF) for highly sensitive and accurate analysis of miRNA in living cells. Compared to the traditional NF system, the developed Ap-TDN-NF system exhibits enhanced stability and improved cellular uptake efficiency due to the incorporation of the 3D nucleic acid nanoshell, reducing false positives. Because the 3D nucleic acid nanoshell hybridizes with the double-stranded probe attached on the surface of gold nanoparticles (AuNPs), it extends the distance between the target recognition sequence of double-stranded and the surface of AuNPs, resulting in improved reaction efficiency and kinetics of the hybridization between the target analyte and the target recognition sequence on the AuNP surface. The Ap-TDN-NF is capable of detecting miR-21 down to as low as 1.2 pM, which is about 780 times more sensitive than the traditional NF system. The Ap-TDN-NF system can also be effectively used for imaging miRNA in living cells with high accuracy. This proposed strategy is expected to become an important tool for nucleic acid imaging and play a significant role in disease diagnosis, treatment, and pharmaceutical research.

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.

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.

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.

Supramolecular Modulator Assisted Cryo-Engineered Porous Cu-DNA Nano-Vehicles for Versatile Theranostic Agent Delivery

DNA nanotechnology combines structural design with therapeutic functions via programmable DNA motifs, but faces challenges in drug loading capacity. Herein a pore-engineering strategy is reported to develop a highly porous, universal DNA nano-vehicle through coordination self-assembly, cryo-engineering, and supramolecular chemistry, adapting to diverse cargo loading with desired theranostic agents. Thus, the complex synthesis and compatibility challenges typically associated with switching between different drug carriers are avoided. To this end, Cu2+ and nucleic acid therapeutic G3139 self-assemble into a prefabricated solid nanostructure, which subsequently undergoes ultrafast freezing and sublimation to introduce porosity, forming highly porous Cu-G3139 nanoparticles (CG NPs). The porous CG NPs efficiently accommodate diverse therapeutic molecules, from chemotherapeutics to non-chemotherapeutic agents, facilitated by positively-charged cyclodextrin. As a proof-of-concept, the photosensitizer indocyanine green (ICG) is loaded and coated with tannic acid (TA) to form CICG@TA, enabling remarkable photothermal and fluorescence imaging-guided synergistic tumor ablation. This work represents the first demonstration of sublimation-induced pore formation in metal-DNA hybrid nanoparticles without chemical etching, offering a scalable "plug-and-play" platform for personalized cancer therapy without redesign. This versatile pore-engineering strategy, merging supramolecular chemistry with cryo-engineered porosity, opens up new avenues for efficient, customized multidrug delivery for diverse tumor theranostic applications.

DNA Nanomaterial-Based Electrochemical Biosensors for Clinical Diagnosis

Sensitive and quantitative detection of chemical and biological molecules for screening, diagnosis and monitoring diseases is essential to treatment planning and response monitoring. Electrochemical biosensors are fast, sensitive, and easy to miniaturize, which has led to rapid development in clinical diagnosis. Benefiting from their excellent molecular recognition ability and high programmability, DNA nanomaterials could overcome the Debye length of electrochemical biosensors by simple molecular design and are well suited as recognition elements for electrochemical biosensors. Therefore, to enhance the sensitivity and specificity of electrochemical biosensors, significant progress has been made in recent years by optimizing the DNA nanomaterials design. Here, the establishment of electrochemical sensing strategies based on DNA nanomaterials is reviewed in detail. First, the structural design of DNA nanomaterial is examined to enhance the sensitivity of electrochemical biosensors by improving recognition and overcoming Debye length. In addition, the strategies of electrical signal transduction and signal amplification based on DNA nanomaterials are reviewed, and the applications of DNA nanomaterial-based electrochemical biosensors and integrated devices in clinical diagnosis are further summarized. Finally, the main opportunities and challenges of DNA nanomaterial-based electrochemical biosensors in detecting disease biomarkers are presented in an aim to guide the design of DNA nanomaterial-based electrochemical devices with high sensitivity and specificity.

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

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

Rectifying artificial nanochannels with multiple interconvertible permeability states

Transmembrane channels play a vital role in regulating the permeation process, and have inspired recent development of biomimetic channels. Herein, we report a class of artificial biomimetic nanochannels based on DNAzyme-functionalized glass nanopipettes to realize delicate control of channel permeability, whereby the surface wettability and charge can be tuned by metal ions and DNAzyme-substrates, allowing reversible conversion between different permeability states. We demonstrate that the nanochannels can be reversibly switched between four different permeability states showing distinct permeability to various functional molecules. By embedding the artificial nanochannels into the plasma membrane of single living cells, we achieve selective transport of dye molecules across the cell membrane. Finally, we report on the advanced functions including gene silencing of miR-21 in single cancer cells and selective transport of Ca2+ into single PC-12 cells. In this work, we provide a versatile tool for the design of rectifying artificial nanochannels with on-demand functions.