查找使用阿拉丁产品的科研文献

CRISPR/Cas14a-based logic system for intelligent microplastic monitoring based on multiple DNA walking mechanisms

Xiaoya Ren,Xu Cui,Ying Zeng,Yimei Guo,Junhua Chen,Jiafeng Pan

In this research article, an intelligent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas14a-based logic system was developed for microplastic monitoring on the basis of catalytic hairpin assembly (CHA) and DNA walkers on magnetic beads. Polyvinyl chloride (PVC) and polystyrene (PS) can activate the CHA-DNA walker sensing system to generate numerous single-stranded DNA fragments that can be recognized by Cas14a. After the cleavage reaction targeting the fluorophore-quencher reporter, a high Cy5 signal can be observed. The fluorescent biosensor is ultrasensitive, with a limit of detection of 3.4 ng/ml for PVC and 4.1 ng/ml for PS. Using PVC and PS as the two inputs, an OR logic gate was further developed. The input combinations of (10), (01), and (11) can give an output of 1. The sensing system is robust and can work in real water samples with good accuracy. Our proposed biosensor can provide an ultrasensitive and intelligent tool for microplastic monitoring.

Efficient double-stranded hydrolysis of plasmid DNA by molybdenum sulfide quantum dots under mild conditions

Xinyu Zhang,Jiashuo Li,Zhifang Wu,Ziying Yan,Xin Tian,Cuicui Ge

The development of inorganic DNA-cleavage reagents has been an area of active research. However, despite extensive efforts, an efficient method for degrading DNA, such as antibiotic resistance genes (ARGs), has not yet been developed because of its high hydrolytic stability. Herein, we present our results demonstrating that molybdenum sulfide quantum dots (MoS 2 QDs) can effectively catalyze the cleavage and degradation of double-stranded DNA under mild conditions (pH 7.4, 37 °C) without requiring external energy. Notably, structure-activity analysis indicates that the nuclease-mimicking activity of the MoS 2 QDs is attributed to the cooperative effects of their crystal structure (phase), sulfur vacancies (S-vacancies), and Lewis acidity. Superior DNA nuclease activity is achieved in the 1T-phase MoS 2 QDs with a higher density of S-vacancies. Unexpectedly, biochemical assays reveal that MoS 2 QDs cleave DNA through phosphate ester hydrolysis, rather than through reactive oxygen species-mediated oxidation, functioning as DNA hydrolases. Furthermore, we demonstrate that MoS 2 QDs significantly suppress the horizontal transfer of ARGs. This study provides a strategy for designing nanozymes with nuclease activities, advancing their development as a new class of agents for eliminating environmental ARGs and preventing the emergence of resistant bacteria.

Development of silicon-on-insulator-based nanoporous silicon photonic crystals for label-free DNA detection

Xiaoyi Lv,Furu Zhong,Zhenhong Jia,Liangliang Chen,Ji Ma,Hongyan Zhang,Zhuangqi Cao,Jun Zhou

We fabricated a one-dimensional nanoporous silicon photonic crystal on a silicon insulator substrate by a cost-effective electrochemical method as an optical biosensor for the detection of DNA hybridization. In the first step, a transfer matrix method was used to calculate the corresponding reflectivity spectrum for the design of nanoporous silicon photonic crystals. Then silicon-on-insulator-based photonic crystals were prepared by a novel simple electrochemical etching. Genes were hybridized inside the porous silicon (PS) pores by aminopropyltriethoxysilane and glutaraldehyde and detected through frequency resolved reflectance measurements. A detection sensitivity of 17.445  nm/μM is demonstrated with good specific detection. The linear response range covers a concentration range of antifreeze protein gene from 0.625 to 10.000 μM. This high responsivity indicates that the silicon-on-insulator-based PS photonic crystal has significant potential for application in biological micro-electro-mechanical-systems technologies.

Primer-Disk-Enabled DNA Data Storage System with Index and Record-Many-Read-Many Features

Jiaxiang Ma,Yu Yang,Ben Pei,Shengli Mi,Zhuo Xiong,Liliang Ouyang

DNA data storage has emerged as a promising information storage technology by encoding information down to base molecules. However, it remains a challenge to structure the DNA data with ease of recording, retrieving, and reading. Here, a primer-disk-enabled hierarchical DNA data storage system is introduced, which allows for the multiple immobilizations of DNA molecules and the generation of corresponding QR codes for retrieving. The primer disk is pre-engineered to present multiple primers, on which encoded DNA molecules with complementary primers can be covalently immobilized on demand via solid-phase PCR. Each DNA file can be retrieved by inkjet printing a fluorescent QR code. A primer disk with up to 10 primers is used. The results show that different DNA files can be subsequently stored on the disk. One can have readily access to the index via fluorescent QR codes and decode information after sequent imaging, convention, and recognition. To this end, the recorded DNA files can be randomly read via solid-phase PCR with sufficient copies of collected DNA for up to 20 reads. Together, this work provides a new DNA data storage system with index and record-many-read-many features, paving the way for the practical use of DNA data storage.

A Rapid Electrochemical DNA Biosensor for Serum Uric Acid Using the Pre-equilibrium Binding Mechanism

Zhenglian Li,Ge Gao,Yanguan Lv,Yingjie Zhang,Haihui Wang,Biwu Liu

The precise and rapid detection of uric acid (UA) in human serum is pivotal for diagnosing and managing metabolic disorders such as gout, kidney disease, and hyperuricemia. However, current equilibrium-based assays suffer from long incubation time, interference from serum components, and a narrow dynamic range. Herein, we present a robust electrochemical DNA assay (EC-DNA) that can respond rapidly (within 1 min) to serum UA under pre-equilibrium conditions, with an extended dynamic range (1–1000 μM). Our assay employs a Mg2+-dependent UA aptamer that can form a metastable hairpin-like structure, allowing for rapid UA binding. The reaction mechanism was validated using electron transfer rate measurements, electrochemical melting experiments, and urea-induced denaturation assays. This pre-equilibrium approach minimizes nonspecific protein adsorption and signal decay, ensuring reliable detection in complex biofluids such as serum and saliva. Our sensor demonstrated a strong correlation with commercial colorimetric assays (Pearson r = 0.947) and successfully differentiated UA levels between healthy individuals and gout patients. Overall, our EC-DNA assay not only presents a rapid and robust method to detect UA in complex biological samples but also provides valuable insights into DNA binding assays under pre-equilibrium conditions.

A CRISPR-Customizable Copper-Coordinated DNA Nanoplatform Potentiates Cuproptosis Through Circadian and Metabolic Pathway Manipulation

Wenxian Zhang,Zhi-Yuan Feng,Zhe Feng,Rui Lian,Zheng Liu,Jingjing Zhang

Despite the promise of cuproptosis in antitumor therapy, developing strategies to enhance its therapeutic efficacy within the tumor microenvironment remains a challenge. Inspired by the chronotherapy that manipulate circadian rhythms to enhance drug effectiveness, herein we report for a CRISPR-customized copper-DNA nanoplatform (Cu-RNP) that synergistically induces multimodal cell death, including potentiated cuproptosis, by manipulating circadian and metabolic pathways. Cu-RNP integrates coordination-driven self-assembly of Cu2+-DNA nanospheres with Cas13d/crRNA ribonucleoproteins targeting BMAL1. Upon cellular internalization, the acidic and reducing endo/lysosomal environment triggers Cu-RNP disassembly, releasing RNP to silence BMAL1 and disrupt circadian oscillations, leading to WEE1 downregulation and p21 upregulation, thereby inducing apoptosis. Simultaneously, liberated Cu2+ generates cytotoxic hydroxyl radicals for chemodynamic therapy (CDT) and concurrently depletes GSH, promoting mitochondrial copper overload for cuproptosis. Importantly, we demonstrate that silencing BMAL1 disrupts circadian rhythms, inhibits glycolysis, enhances mitochondrial respiration, and redirects metabolic flux to the TCA cycle, thereby amplifying the cell’s vulnerability to copper-induced cuproptosis. In vitro and in vivo results demonstrate that Cu-RNP sensitizes cancer cells to cuproptosis and elicit strong antitumor response through the synergistic combination of cuproptosis, CDT, apoptosis, and circadian-metabolic modulation. This study demonstrates a mechanistic link between BMAL1-regulated circadian rhythms and cuproptosis sensitivity, suggesting a potential treatment strategy for multimodal, cuproptosis-potentiating cancer therapies.

Mitochondrial DNA-boosted dendritic cell-based nanovaccination triggers antitumor immunity in lung and pancreatic cancers

Lihuan Shang,Xue Jiang,Xinbao Zhao,Xi Huang,Xiaojuan Wang,Xue Jiang,Xiangzhan Kong,Mingkang Yao,Shanping Jiang,Ping-Pui Wong

Low migratory dendritic cell (DC) levels pose a challenge in cancer immune surveillance, yet their impact on tumor immune status and immunotherapy responses remains unclear. We present clinical evidence linking reduced migratory DC levels to immune-cold tumor status, resulting in poor patient outcomes. To address this, we develop an autologous DC-based nanovaccination strategy using patient-derived organoid or cancer cell lysate-pulsed cationic nanoparticles (cNPs) to load immunogenic DC-derived microvesicles (cNP cancer cell @MV DC ). This approach transforms immune-cold tumors, increases migratory DCs, activates T cells and natural killer cells, reduces tumor growth, and enhances survival in orthotopic pancreatic and lung cancer models, surpassing conventional methods. In vivo imaging reveals superior cNP cancer cell @MV DC accumulation in tumors and lymph nodes, promoting immune cell infiltration. Mechanistically, cNPs enrich mitochondrial DNA, enhancing cGAS-STING-mediated DC activation and migration. Our strategy shifts cold tumors to a hot state, enhancing antitumor immunity for potential personalized cancer treatments.

DNA damage protection and 5-lipoxygenase inhibiting activity of areca (Areca catechu L.) inflorescence extracts

W Chen,C Zhang,Y Huang,F Cheng,S Zhao,Y Shen,J Liu

Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments

Ying Wang,Yuehua Hu,Tao Wu,Lihua Zhang,Hua Liu,Xiaoshun Zhou,Yong Shao

Removal of a damaged base in DNA produces an abasic site (AP site) nanocavity. If left un-repaired in vivo by the specific enzyme, this nanocavity will result in nucleotide mutation in the following DNA replication. Therefore, selective recognition of AP site nanocavity by small molecules is important for identification of such DNA damage and development of genetic drugs. In this work, we investigate the fluorescence behavior of isoquinoline alkaloids including palmatine (PAL), berberine (BER), epiberberine (EPI), jatrorrhizine (JAT), coptisine (COP), coralyne (COR), worenine (WOR), berberrubine (BEU), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT) upon binding with the AP nanocavity. PAL is screened out as the most efficient fluorophore-switched probe to recognize the AP nanocavity over the fully matched DNA. Its fluorescence enhancement occurs for all of the AP nanocavity sequence environments, which has not been achieved by the previously used probes. The bridged π conjugation effect should partially contribute to the AP nanocavity-specific fluorescence, as opposed to the solvent effect . Due to the strong binding with the AP nanocavity, PAL will find wide applications in the DNA damage recognition and sensor development.

Antifouling Electrochemical Biosensor Based on Conductive Hydrogel of DNA Scaffold for Ultrasensitive Detection of ATP

Xiaoyan He,Nan Sun,Hui Jia,Miaomiao Hou,Zheping Tan,Xiaoquan Lu

As an energy supplier, ATP plays an important role in various life activities, and there is an urgent need to develop an effective means of detecting ATP. However, the traditional sensors face serious nonspecific adsorption. In this work, an antifouling electrochemical biosensor based on the interpenetrating network of Y-DNA scaffold and polyaniline hydrogel was designed for ATP detection. The polyaniline hydrogel was conducive to the transport of electrons and ions, the structure of Y-DNA cross-linked by ATP aptamers in the polyaniline hydrogel achieved the effect of signal amplification. Super hydrophilic cellulose nanocrystals (CNCs) and zwitterion polypeptide sequence (Pep) were doped to play a synergistic antifouling effect. The hydrogel sensor we have built has a wide linear range of 0.1 pM–1 μM for ATP detection and a low detection limit of 0.025 pM (S/N = 3). For ATP detection in actual serum samples, the recovery of this sensor was 99.5%–106%, and the relative standard deviation was 0.4%–2.88%. It is proven that the sensor has good ATP detection performance, and it will provide a certain reference value for the detection of other biological small molecules.

Biocompatible nucleus-targeted graphene quantum dots for selective killing of cancer cells via DNA damage

Qi Lei,Pan Tonghe,Ou Liling,Ye Zhiqiang,Yu Chunlei,Bao Bijun,Wu Zixia,Cao Dayong,Dai Liming

Graphene quantum dots (GQDs) are nano-sized graphene slices. With their small size, lamellar and aromatic-ring structure, GQDs tend to enter into the cell nucleus and interfere with DNA activity. Thus, GQD alone is expected to be an anticancer reagent. Herein, we developed GQDs that suppress the growth of tumor by selectively damaging the DNA of cancer cells. The amine-functionalized GQDs were modified with nucleus targeting TAT peptides (TAT-NGs) and further grafted with cancer-cell-targeting folic acid (FA) modified PEG via disulfide linkage (FAPEG-TNGs). The resulting FAPEG-TNGs exhibited good biocompatibility, nucleus uptake, and cancer cell targeting. They adsorb on DNA via the π–π and electrostatic interactions, which induce the DNA damage, the upregulation of the cell apoptosis related proteins, and the suppression of cancer cell growth, ultimately. This work presents a rational design of GQDs that induce the DNA damage to realize high therapeutic performance, leading to a distinct chemotherapy strategy for targeted tumor therapy.

Titanium dioxide nanoparticles induce size-dependent cytotoxicity and genomic DNA hypomethylation in human respiratory cells

Yue Ma,Yinsheng Guo,Shuang Wu,Ziquan Lv,Qian Zhang,Yuebin Ke

The widespread use of titanium dioxide nanoparticles (TiO2 NPs) is gradually increasing the risk of exposure to these potentially hazardous materials. Although numerous health effects of TiO2 NPs have been investigated, it remains unknown whether they could affect the respiratory cellular epigenome. We explored the viability, membrane integrity, intracellular ROS and genomic DNA methylation of human respiratory cells, as well as their expression of methylation-related genes, after treatment with TiO2 NPs with diameters of 25 nm (nanotube morphology) or 60 nm (anatase morphology). Two cell lines relevant to inhalation exposure, namely human bronchial epithelial cell line (16HBE) and human non-small cell lung cancer cells (A549), were tested, with treatment concentrations ranging from 0.1 to 100 μg mL−1. The TiO2 NPs induced time- and concentration-dependent decreases in cell viability in both A549 and 16HBE cells. The reduction in cell viability was greater for the smaller particles (size 25 nm) of the nanotube type. Cellular membrane integrity assays revealed that 16HBE cells were less sensitive to TiO2 NPs-25 nm (nanotube-type) than were A549 cells, as higher concentrations were required for cytotoxicity against the former. TiO2 NPs-25 nm (nanotube-type) showed greater toxicity against both cell lines than TiO2 NPs-60 nm (anatase-type). Intracellular ROS levels in both A549 and 16HBE cell were increased by TiO2 NPs whereas pretreatment with the antioxidant N-acetyl-L-cysteine eliminated TiO2 NPs-induced ROS accumulation and reduced cell death. Moreover, the anatase-type TiO2 NPs resulted in decreased global DNA methylation and altered expression levels of methylation-related genes and proteins, suggesting that these NPs induce cellular epigenomic toxicity. These results allowed us to confirm the epigenetic mechanism by which TiO2 NPs damage human respiratory cells.