DNA flower-encapsulated horseradish peroxidase with enhanced biocatalytic activity synthesized by an isothermal one-pot method based on rolling circle amplification

Hydrogel-integrated sensors for food safety and quality monitoring: Fabrication strategies and emerging applications

Food safety is a global issue in public hygiene. The accurate, sensitive, and on-site detection of various food contaminants performs significant implications. However, traditional methods suffer from the time-consuming and professional operation, restricting their on-site application. Hydrogels with the merits of highly porous structure, high biocompatibility, good shape-adaptability, and stimuli-responsiveness offer a promising biomaterial to design sensors for ensuring food safety. This review describes the emerging applications of hydrogel-based sensors in food safety inspection in recent years. In particular, this study elaborates on their fabrication strategies and unique sensing mechanisms depending on whether the hydrogel is stimuli-responsive or not. Stimuli-responsive hydrogels can be integrated with various functional ligands for sensitive and convenient detection via signal amplification and transduction; while non-stimuli-responsive hydrogels are mainly used as solid-state encapsulating carriers for signal probe, nanomaterial, or cell and as conductive media. In addition, their existing challenges, future perspectives, and application prospects are discussed. These practices greatly enrich the application scenarios and improve the detection performance of hydrogel-based sensors in food safety detection.

A review of DNA nanoparticles-encapsulated drug/gene/protein for advanced controlled drug release: Current status and future perspective over emerging therapy approaches

In the last ten years, the field of nanomedicine has experienced significant progress in creating novel drug delivery systems (DDSs). An effective strategy involves employing DNA nanoparticles (NPs) as carriers to encapsulate drugs, genes, or proteins, facilitating regulated drug release. This abstract examines the utilization of DNA NPs and their potential applications in strategies for controlled drug release. Researchers have utilized the distinctive characteristics of DNA molecules, including their ability to self-assemble and their compatibility with living organisms, to create NPs specifically for the purpose of delivering drugs. The DNA NPs possess numerous benefits compared to conventional drug carriers, such as exceptional stability, adjustable dimensions and structure, and convenient customization. Researchers have successfully achieved a highly efficient encapsulation of different therapeutic agents by carefully designing their structure and composition. This advancement enables precise and targeted delivery of drugs. The incorporation of drugs, genes, or proteins into DNA NPs provides notable advantages in terms of augmenting therapeutic effectiveness while reducing adverse effects. DNA NPs serve as a protective barrier for the enclosed payloads, preventing their degradation and extending their duration in the body. The protective effect is especially vital for delicate biologics, such as proteins or gene-based therapies that could otherwise be vulnerable to enzymatic degradation or quick elimination. Moreover, the surface of DNA NPs can be altered to facilitate specific targeting towards particular tissues or cells, thereby augmenting the accuracy of delivery. A significant benefit of DNA NPs is their capacity to regulate the kinetics of drug release. Through the manipulation of the DNA NPs structure, scientists can regulate the rate at which the enclosed cargo is released, enabling a prolonged and regulated dispensation of medication. This control is crucial for medications with limited therapeutic ranges or those necessitating uninterrupted administration to attain optimal therapeutic results. In addition, DNA NPs have the ability to react to external factors, including alterations in temperature, pH, or light, which can initiate the release of the payload at precise locations or moments. This feature enhances the precision of drug release control. The potential uses of DNA NPs in the controlled release of medicines are extensive. The NPs have the ability to transport various therapeutic substances, for example, drugs, peptides, NAs (NAs), and proteins. They exhibit potential for the therapeutic management of diverse ailments, including cancer, genetic disorders, and infectious diseases. In addition, DNA NPs can be employed for targeted drug delivery, traversing biological barriers, and surpassing the constraints of conventional drug administration methods.

Dual-mode optical biosensor based on multi-functional DNA structures for detecting bioactive small molecules

Semiconducting polymer dots and hemin-functionalized DNA nanoflowers with excellent peroxidase-like activity and high fluorescent brightness are prepared for fluorescent/colorimetric dual-mode sensing of dopamine and glutathione as low as nM and μM, respectively. This biosensor is readily applied to the analysis of complicated biological samples with high selectivity and accuracy, which opens up promising prospects in clinical applications.

Detection of SARS-CoV-2 receptor binding domain using fluorescence probe and DNA flowers enabled by rolling circle amplification

Using rolling circle amplification (RCA) and two different ways of signal readout, we developed analytical methods to detect the receptor-binding domain (RBD) of SARS-CoV-2 spike protein (S protein). We modified streptavidin-coated magnetic beads with an aptamer of RBD through a biotin-tagged complementary DNA strand (biotin-cDNA). Binding of RBD caused the aptamer to dissociate from the biotin-cDNA, making the cDNA available to initiate RCA on the magnetic beads. Detection of RBD was achieved using a dual signal output. For fluorescence signaling, the RCA products were mixed with a dsDNA probe labeled with fluorophore and quencher. Hybridization of the RCA products caused the dsDNA to separate and to emit fluorescence (λ_ex = 488 nm, λ_em = 520 nm). To generate easily detectable UV-vis absorbance signal, the RCA amplification was extended to produce DNA flower to encapsulate horseradish peroxidase (HRP). The HRP-encapsulated DNA flower catalyzed a colorimetric reaction between H₂O₂ and 3,3',5,5'-tetramethylbenzidine (TMB) to generate an optical signal (λ_abs = 450 nm). The fluorescence and colorimetric assays for RBD have low detection limits (0.11 pg mL^-1 and 0.904 pg mL^-1) and a wide linear range (0.001-100 ng mL^-1). For detection of RBD in human saliva, the recovery was 93.0-100% for the fluorescence assay and 87.2-107% for the colorimetric assay. By combining fluorescence and colorimetric detection with RCA, detection of the target RBD in human saliva was achieved with high sensitivity and selectivity.

A colorimetric and photothermal dual-mode biosensing platform based on nanozyme-functionalized flower-like DNA structures for tumor-derived exosome detection

Tumor-derived exosomes can be served as a kind of promising biomarkers for early diagnosis of cancers. Herein, a colorimetric/photothermal dual-mode exosomes sensing platform is developed for human breast cancer cell (MCF-7)-derived exosomes based on encapsulation of 3,3',5,5'-tetramethylbenzidine-loaded graphene quantum dot nanozymes (TMB-GQDzymes) into DNA flowers (DFs) via rolling circle amplification (RCA). To achieve specific detection, EpCAM aptamer for MCF-7 cell-derived exosomes is immobilized on the well plate, while the complementary sequence of another CD63 aptamer is designed into the circular template to obtain abundant capture probes. Benefitting from the dual-aptamer recognition strategy, a sandwich structure of EpCAM aptamer/exosomes/TMB-GQDzymes@DFs is formed, in which the GQDzymes can catalyze the oxidation of TMB in the presence of H₂O₂. The resulting products of TMB oxidation (oxTMB) can induce not only the absorption changes but also a near-infrared (NIR) laser-driven photothermal effect, achieving dual-mode detection of exosomes with the limit of detection (LOD) of 1027 particles/μL (colorimetry) and 2170 particles/μL (photothermal detection), respectively. In addition, this sensing platform has demonstrated excellent performance to well distinguish breast cancer patients from healthy individuals in serum samples analysis. Overall, the proposed dual-readout biosensor opens promising prospects for exosome detection in biological study and clinical applications.

A Synergistic Dual-Channel Sensor for Ultrasensitive Detection of Pseudomonas aeruginosa by DNA Nanostructure and G-Quadruplex

Pseudomonas aeruginosa is one of the foodborne pathogenic bacteria that greatly threatens human health. An ultrasensitive technology for P. aeruginosa detection is urgently demanded. Herein, based on the mechanism of aptamer-specific recognition, an electrochemical-colorimetric dual-mode ultrasensitive sensing strategy for P. aeruginosa is proposed. The vertices of DNA tetrahedral nanoprobes (DTNPs), that immobilized on the gold electrode were modified with P. aeruginosa aptamers. Furthermore, the G-quadruplex, which was conjugated with a P. aeruginosa aptamer, was synthesized via rolling circle amplification (RCA). Once P. aeruginosa is captured, a hemin/G-quadruplex, which possesses peroxidase-mimicking activity, will separate from the P. aeruginosa aptamer. Then, the exfoliated hemin/G-quadruplexes are collected for oxidation of the 3,3',5',5'-tetramethylbenzidine for colorimetric sensing. In the electrochemical mode, the hemin/G-quadruplex that is still bound to the aptamer catalyzes polyaniline (PANI) deposition and leads to a measurable electrochemical signal. The colorimetric and electrochemical channels demonstrated a good forward and reverse linear response for P. aeruginosa within the range of 1-10⁸ CFU mL^-1, respectively. Overall, compared with a traditional single-mode sensor for P. aeruginosa, the proposed dual-mode sensor featuring self-calibration not only avoids false positive results but also improves accuracy and sensitivity. Furthermore, the consistency of the electrochemical/colorimetric assay was verified in practical meat samples and showed great potential for applications in bioanalysis.

DNA-Mediated Control of Protein Function in Semi-Synthetic Systems

The development of strategies for controlling protein function in a precise and predictable manner has the potential to revolutionize catalysis, diagnostics, and medicine. In this regard, the use of DNA has emerged as a powerful approach for modulating protein activity. The programmable nature of DNA allows for constructing sophisticated architectures wherein proteins can be placed with control over position, orientation, and stoichiometry. This ability is especially useful considering that the properties of proteins can be influenced by their local environment or their proximity to other functional molecules. Here, we chronicle the different strategies that have been developed to interface DNA with proteins in semi-synthetic systems. We further delineate the unique applications unlocked by the unprecedented level of structural control that DNA affords. We end by outlining outstanding challenges in the area and discuss future research directions towards potential solutions.

Strategies for Enhancing the Sensitivity of Electrochemiluminescence Biosensors

Electrochemiluminescence (ECL) has received considerable attention as a powerful analytical technique for the sensitive and accurate detection of biological analytes owing to its high sensitivity and selectivity and wide dynamic range. To satisfy the growing demand for ultrasensitive analysis techniques with high efficiency and accuracy in complex real sample matrices, considerable efforts have been dedicated to developing ECL strategies to improve the sensitivity of bioanalysis. As one of the most effective approaches, diverse signal amplification strategies have been integrated with ECL biosensors to achieve desirable analytical performance. This review summarizes the recent advances in ECL biosensing based on various signal amplification strategies, including DNA-assisted amplification strategies, efficient ECL luminophores, surface-enhanced electrochemiluminescence, and ratiometric strategies. Sensitivity-enhancing strategies and bio-related applications are discussed in detail. Moreover, the future trends and challenges of ECL biosensors are discussed.

DNA-directed coimmobilization of multiple enzymes on organic−inorganic hybrid DNA flowers

The artificial multienzyme systems developed by mimicking nature has attracted much interest. However, precisely controlled compositions and ratios of multienzymatic co-immobilization systems are still limited by the indistinguishable nature of enzymes. Herein, a strategy for fabricating DNA-directed immobilization of horseradish peroxidase (HRP) and glucose oxidase (GOx) on hybrid DNA nanoflowers (GOx-HRP@hDFs) is presented. The preparation of micron-sized hybrid DNA flowers (hDFs) begins with the predetermined repeatable polymer-like DNA sequences which contained two strands. The hDFs structure is generated through one-pot rolling circle amplification (RCA) and self-assembly with magnesium pyrophosphate inorganic crystals. Based on the rigid-base pairing, GOx and HRP conjugated with sequences complementary to strands would be anchored to the predesigned locations, respectively. By adjusting the loading amount/ratio of enzymes properly, the maximal catalytic efficiency can be precisely regulated. The reaction activity of GOx-HRP@hDFs was 7.4 times higher than that of the free GOx-HRP under the optimal mole ratio (GOx/HRP 4:1). In addition, this multienzyme catalyst system exhibits excellent precision, specificity, reproducibility, and long-term storage stability when applied to real human blood samples. The preceding results validate that GOx-HRP@hDFs are promising candidates for personal diabetes detection.

Sensitive Detection of Staphylococcus aureus by a Colorimetric Biosensor Based on Magnetic Separation and Rolling Circle Amplification

Staphylococcus aureus (S. aureus) is a common foodborne pathogen that causes fever, vomiting, and other intestinal symptoms, and seriously affects human health and social safety. As a result, a reliable and sensitive detection technique for S. aureus must be developed. In this work, we proposed a sandwich assay on vancomycin functionalized magnetic beads (Van-MNPs) for S. aureus detection based on the specific binding between IgG and targets. The Van-MNPs were used as a tool for the separation of target bacteria. The biotin-modified IgG mediates binding between DNA nanoflowers (DNFs) and the target bacteria via interacting with streptavidin. The DNFs prepared by rolling circle amplification (RCA) were employed as a nano-container to enhance the capacity of biotins, and the streptavidin-horseradish peroxidase (SA-HRP) was loaded onto DNFs to catalyze the color change of TMB. Therefore, a colorimetric biosensor based on magnetic separation and rolling circle amplification was developed. The proposed methods for S. aureus detection showed a limit of detection (LOD) of 3.3 × 10³ CFU/mL and excellent specificity. The biosensor has a certain reference value for the detection of S. aureus in juice.

A nanozyme-based colorimetric sensor array as electronic tongue for thiols discrimination and disease identification

Thiol analysis is of vital significance due to the essential roles in disease diagnosis, while the highly similar structures of thiols are a major challenge in practical determination. Herein, a nanozyme-based colorimetric sensor array has been proposed as electronic tongue for excellent discrimination and sensitive quantitation of thiols. The sensing units are fabricated by integrating the terephthalic acid modified graphene quantum dots (TPA@GQDs) with three transition metal ions (Fe²⁺, Cu²⁺ and Zn²⁺) via coordination, respectively, which not only provide sufficient substrate binding sites but also form the metal ion-regulated catalytic active centers. In this way, disparate promotion degrees on the peroxidase-like catalytic activity have been achieved in different metal ion-TPA@GQD ensembles. Based on the strong binding affinity between metal ions and thiols, the catalytic active centers are removed from TPA@GQDs, which inhibits the catalytic activity of sensing unit to diverse degrees. Accordingly, using 3, 3', 5, 5'-tetramethylbenzidine (TMB) as chromogenic substrate in the presence of hydrogen peroxide (H₂O₂), each sensing unit can generate differential colorimetric signals (fingerprints) for six thiol analytes, which can be accurately discriminated through linear discriminant analysis (LDA) with a detection limit of 50 nM. In addition, the discrimination of the same thiol with different concentrations and thiol mixtures have also been achieved. Furthermore, inspired by the distinct levels of thiols in practical samples, the proposed sensor array enables the identification of thiol-associated diseases by means of machine learning algorithm, which makes a positive contribution to medical diagnosis.

A novel aptasensor based on DNA hydrogel for sensitive visual detection of ochratoxin A

A novel visual detection mode is proposed to improve the detection sensitivity for the determination of ochratoxin A (OTA). The mode is based on aptamer recognition and the signal amplification of rolling circle amplification (RCA) products self-assembled DNA hydrogel. Moreover, gold nanoparticles (AuNPs) were directly assembled inside the DNA hydrogel by adjusting the padlock probe sequences to achieve a stronger binding force between the DNA hydrogel and AuNPs; this avoids the need for modification of AuNPs with DNA sequences. In the presence of OTA, DNA hydrogel is formed. With higher concentrations of OTA, a larger amount of DNA hydrogel is formed. When AuNPs are added to the DNA hydrogel, AuNPs can be enclosed inside the DNA hydrogel. With more DNA hydrogel, there is less AuNPs in the supernatant. Thus, the absorbance of the supernatant is anti-correlated with the concentration of OTA. After optimization of the experimental conditions, the change in the absorbance of the supernatant was linearly correlated with the concentration of OTA, in the range 0.05 to 10 ng/mL; the limit of detection was 0.005 ng/mL. The good specificity of the developed biosensor was confirmed in the presence of other mycotoxins that are coexistent with or analogues of OTA. By comparing the developed method with the ELISA method, the accuracy and stability of this new method were also verified, with good performance obtained in real samples. Diagram of the principle of the colorimetric aptasensor for OTA detection based on rolling circle amplification product self-assembled DNA hydrogel.

Graphene-coated copper-doped ZnO quantum dots for sensitive photoelectrochemical bioanalysis of thrombin triggered by DNA nanoflowers

This work reports a photoelectrochemical (PEC) biosensing platform for the sensitive and specific screening of thrombin by using graphene oxide-coated copper-doped zinc oxide quantum dots (Cu_0.3Zn_0.7O-GO QDs) as the photoactive materials and glucose oxidase-encapsulated DNA nanoflowers (GOx-DFs) for signal amplification. Interestingly, the coated graphene oxide nanosheets on the surface of the Cu_0.3Zn_0.7O QDs could cause the charge to transfer rapidly and ameliorate the photocorrosion. The doped copper into the quantum dots could enhance the absorption of visible light by tuning the band gap of ZnO QDs, therefore increasing the photocurrent under visible irradiation. Upon addition of target thrombin, a sandwiched reaction was carried out between thrombin aptamer and GOx-DFs, accompanying the formation of nanocomposites with the magnetic microparticles (MMPs)/thrombin/GOx-DFs. Followed by magnetic separation, the carried GOx oxidized glucose to H₂O₂, thus resulting in the increasing photocurrent of the Cu_0.3Zn_0.7O-GO QD-modified electrode. Under optimum conditions, the developed PEC biosensing platform exhibited good analytical performance with a linear range of 50-10 000 fM thrombin and a limit of detection of 29 fM. Impressively, our strategy offers a new horizon in developing bridge-connected graphene-coated nanomaterials and novel signal amplification strategy for the development of PEC biosensors.

Enzymatically Active DNA-Protein Nanogels with Tunable Cross-Linking Density

Hybrid DNA-protein nanogels represent potential protein vectors and enzymatic nanoreactors for modern biotechnology. Here, we describe a new, easy, and robust method for preparation of tunable DNA-protein nanogels with controllable size and density. For this purpose, polymerase chain reaction is used to prepare highly biotinylated DNA as a soft biopolymeric backbone, which can be efficiently cross-linked via streptavidin-biotin binding. This approach enables us to control both the density and size of the resulting nanogels not only by adjusting the amount of the cross-linking streptavidin but also by using different rates of DNA biotinylation. This gives DNA-streptavidin nanogels with the size ranging from 80 nm, for the most compact state, to up to 200 nm. Furthermore, using streptavidin-enzyme conjugates allows the straightforward one-pot incorporation of enzymes during the preparation of the nanogels. Monoenzymatic and multienzymatic nanogels have been obtained in this manner, and their catalytic activities have been characterized. All tested enzymes (alkaline phosphatase (AP), horseradish peroxidase (HRP), and β-galactosidase (βGal)), incorporated individually or in a coupled manner (glucose oxidase (GOx)-HRP cascade), were shown to remain functional. The activities of AP and βGal were unchanged while that of HRP was slightly improved inside the nanogels. We demonstrate that, for HRP, it is not the DNA-to-enzyme ratio but the physical density of the functionalized DNA nanogels that is responsible for the improvement of its enzymatic activity.

Point-of-care diagnostics for infectious diseases: From methods to devices

The current widespread of COVID-19 all over the world, which is caused by SARS-CoV-2 virus, has again emphasized the importance of development of point-of-care (POC) diagnostics for timely prevention and control of the pandemic. Compared with labor- and time-consuming traditional diagnostic methods, POC diagnostics exhibit several advantages such as faster diagnostic speed, better sensitivity and specificity, lower cost, higher efficiency and ability of on-site detection. To achieve POC diagnostics, developing POC detection methods and correlated POC devices is the key and should be given top priority. The fast development of microfluidics, micro electro-mechanical systems (MEMS) technology, nanotechnology and materials science, have benefited the production of a series of portable, miniaturized, low cost and highly integrated POC devices for POC diagnostics of various infectious diseases. In this review, various POC detection methods for the diagnosis of infectious diseases, including electrochemical biosensors, fluorescence biosensors, surface-enhanced Raman scattering (SERS)-based biosensors, colorimetric biosensors, chemiluminiscence biosensors, surface plasmon resonance (SPR)-based biosensors, and magnetic biosensors, were first summarized. Then, recent progresses in the development of POC devices including lab-on-a-chip (LOC) devices, lab-on-a-disc (LOAD) devices, microfluidic paper-based analytical devices (μPADs), lateral flow devices, miniaturized PCR devices, and isothermal nucleic acid amplification (INAA) devices, were systematically discussed. Finally, the challenges and future perspectives for the design and development of POC detection methods and correlated devices were presented. The ultimate goal of this review is to provide new insights and directions for the future development of POC diagnostics for the management of infectious diseases and contribute to the prevention and control of infectious pandemics like COVID-19.

Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials

The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.

Circular Nucleic Acids: Discovery, Functions and Applications

Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.

Enhanced electrochemiluminescence of luminol based on Cu2O-Au heterostructure enabled multiple-amplification strategy

Herein, a credible construction strategy to improve electrochemiluminescence (ECL) of luminol was developed based on Cu₂O-Au heterostructures. Summarily, gold nanoparticles (AuNPs) were anchored on surface of Cu₂O nanocube (Cu₂O@AuNPs) by spontaneous reduction reaction. Then, luminol molecules were concentrated on Cu₂O@AuNPs using L-Cysteine (Cys) as covalent linkage to build the composite emitter (Cu₂O@AuNPs-Cys-luminol). The enhancement mechanism was realized by following aspects: (I) Cu₂O@AuNPs worked as electrocatalyst for glucose to generate coreactant of H₂O₂ in situ, avoiding the instability of direct addition of H₂O₂. (II) luminol molecules were firmly attached on Cu₂O@AuNPs to achieve centralized and strong luminescence at low consumption. (III) Cys acted as an intramolecular coreactant and directly linked to luminol to increase luminous efficiency. To validate the effectiveness, a sandwiched immunoassay was built using concanavalinA (ConA) as analyte. Electroreduced graphene film as substrate provided phenoxy-derivatized dextran (DexP) with abundant binding sites and improved conductivity. To improve the specificity, DexP was used to identify ConA via the specific carbohydrate-ConA interaction. Then, Cu₂O@AuNPs-Cys-luminol was modified on electrode as ECL signal indicator. The ECL immunosensor achieved determination of ConA with low detection limit of 2.9 × 10^-5 ng/mL and excellent stability of continuous potential scan for 8 cycles. Experimental results demonstrated that the proposed construction strategy made considerable progress in ECL efficiency and stability of luminol. The creational pattern of construction strategy achieves high detection capabilities to ConA and expands the applicability of luminol in ECL system. It is expected to have more potential application value in immunoassay with universality.

A single-molecule study reveals novel rod-like structures formed by a thrombin aptamer repeat sequence

Thrombin aptamers (TBAs) have attracted much attention due to their various applications. The structures and properties of long ssDNA chains with multiple TBA repeat sequences are interesting and distinct from those of their monomers. Due to the complexity of the sample system, it is quite difficult to reveal the structure of such a long-chain ssDNA using traditional methods. In this work, we investigated the repeated ssDNA by using single-molecule magnetic tweezers and AFM imaging. To do that we developed the polymerase change-rolling circle amplification (PC-RCA) synthetic method and prepared two-end modified repeated ssDNA. The rod-like G4 structures formed by intramolecular stacking of the repeat sequence were for the first time identified. This novel structure is different from those higher-order quadruplex structures formed by G-tetrads or loop-mediated interactions. It is also quite interesting to find that the increase of the TBA copy number can unitize the diversity of TBA conformation to the best-fit binding structure for thrombin. The methodology developed in this work can be used for studying other repeat sequences in the genome, such as telomeric DNA as well as interactions of ssDNA with the binding molecule.

A Fluorescent DNA Hydrogel Aptasensor Based on the Self-Assembly of Rolling Circle Amplification Products for Sensitive Detection of Ochratoxin A

A sensitive fluorescent DNA hydrogel aptasensor based on the self-assembly of rolling circle amplification (RCA) products was developed for ochratoxin A (OTA) detection in beer. A competitive binding mode of aptamer, complementary sequence, and target was integrated into the DNA hydrogel for OTA detection. The OTA aptamer first combined with the primer to form the hybridized product. Then, in the presence of OTA, the aptamer combined with OTA, which released the primer. The released primer hybridized with the padlock probe to form a circular template, and the RCA reaction was initiated by adding ligase, polymerase, and dNTPs. The fluorescent DNA hydrogel was obtained by adding Cy3-dUTP together with dNTPs, and the fluorescence (FL) intensity of the DNA hydrogel was positively correlated with OTA concentration. Under the optimal experimental conditions, the linear range of the relationship varied from 0.05 ng/mL to 100 ng/mL with a detection limit for OTA of 0.01 ng/mL. The fluorescent DNA hydrogel aptasensor showed good specificity and stability in beer samples. Therefore, the fabricated DNA hydrogel aptasensor shows considerable potential applications in detecting OTA for food safety.

Highly-branched Cu2O as well-ordered co-reaction accelerator for amplifying electrochemiluminescence response of gold nanoclusters and procalcitonin analysis based on protein bioactivity maintenance

The point of fabricating ultrasensitive electrochemiluminescence (ECL)-based biosensors should be focused on how to maintain high immune recognition of antigens by antibodies in whole process. That is not effortless due to the structure of the protein can be destroyed root in toxic nanocarriers, excessive cyclic potential and superoxide radicals in coreactant, all of which can lead to reduce the bioactivity of antigen and antibody. In this work, the effect of negative voltage and divers coreactant on protein bioactivity were verified. Based on that, a motivated ECL biosensor with good biocompatibility was fabricated for procalcitonin (PCT) detection using Au nanoclusters (Au NCs) as low-potential cathodic luminophor and K₂S₂O₈ as non-toxic coreactant, respectively. Besides, highly-branched Cu₂O was utilized to catalyze K₂S₂O₈ and produce more radical anion SO₄^•-, which can oxidize Au NCs^•- to generate more high-energy-state Au NCs*, thus doubling the ECL intensity to meet the requirements of trace analysis. In addition, protein A (PA) as specific antibody capturer was employed to bind the Fc region of anti-PCT in an orientated way, further maintaining the physiological activity of antibody. As expected, all strategies undoubtedly practically improved the immune recognition of the biosensor and reduced the detection limit to 2.90 fg/mL.

Visualization of the intracellular location and stability of DNA flowers with a label-free fluorescent probe

Rolling circle amplification (RCA) and rolling circle transcription (RCT) can be used to fabricate various structures and organize functional materials for biological applications. The full understanding of the interactions between RCA/RCT-derived structures and live cells is urgently demanded. Here, we present a label-free fluorescent strategy to study the intracellular location and stability of RCA-based DNA flowers in live cells. The DNA flower structures are co-assembled with carbazole-based biscyanine fluorophores, which are DNA detecting molecules and characterized by restriction of intramolecular rotation (RIR) induced strong fluorescent emission. When biscyanine molecules are encapsulated in the DNA flowers via electrostatic attraction, these confined RIR dyes can produce strong luminescent emission. Using this advantage, we use the RIR enhanced technique for direct visualization of the distribution and degradation of DNA flowers in live cellular systems. Our current research could be adapted to other advanced DNA-based materials, providing a new strategy to fabricate fluorescent DNA materials and realize controllable release of payloads.

Microfluidic paper-based photoelectrochemical sensing platform with electron-transfer tunneling distance regulation strategy for thrombin detection

This work reports a microfluidic paper-based photoelectrochemical (μ-PEC) sensing platform for thrombin (TB) detection with electron-transfer tunneling distance regulation (ETTDR) and aptamer target-triggering nicking enzyme signaling amplification (NESA) dual strategies. Specifically, paper-based TiO₂ nanosheets (PTNs) were prepared with an efficient hydrothermal process, serving as the direct pathway for the charge carriers transfer. When CeO₂-labeled hairpin DNA 3 (HP3) was closely located at the PTNs, the CeO₂-PTNs heterostructure was formed, which could great facilitate the photogenerated carries separation of CeO₂. In addition, with the aid of aptamer target-triggering NESA strategy, the input TB could be transducted to numerous output target of DNA (tDNA), achieving the goal of desirable signal amplification. In the presence of TB, the output tDNA could be further hybridized with HP3 and unfold its hairpin loop, which forced the CeO₂ away from the surface of PTNs and vanished the CeO₂-PTNs heterostructure, resulting in the obviously reducing of photocurrent signal. The as-designed sensing platform exhibited a linear range from 0.02 pM to 100 pM with a detection limit of 6.7 fM. Importantly, this μ-PEC sensing platform could not only realize the highly efficient TB detection, but also pave a luciferous way for the detection of other protein in bioanalysis.

Porphyrin functionalized Co(OH)2/GO nanocomposites as an excellent peroxidase mimic for colorimetric biosensing

A colorimetric sensor based on the enhanced peroxidase-like activity of Por/Co(OH)₂/GO for the sensitive detection of H₂O₂ and GSH.