keyword
https://read.qxmd.com/read/38457281/dynamic-assembly-of-dna-nanostructures-in-cancer-cells-enables-the-coupling-of-autophagy-activating-and-real-time-tracking
#21
JOURNAL ARTICLE
Yanfei Guo, Zhaobin Tong, Yan Huang, Jianpu Tang, Xue Xue, Dayong Yang, Chi Yao
Developing dynamic nanostructures for in situ regulation of biological processes inside living cells is of great importance in biomedical research. Herein we report the cascaded assembly of Y-shaped branched DNA nanostructure (YDN) during intracellular autophagy. YDN contains one arm with semi-i-motif sequence and Cy3-BHQ2, and another arm with an apurinic/apyrimidinic (AP) site and Cy5-BHQ3. Upon uptake by cancer cells, intermolecular i-motif structures are formed in response to lysosomal H+ , causing the formation of YDN-dimer and the recovery of Cy3 fluorescence; when escapes occur from the lysosome to the cytoplasm, the YDN-dimer responds to the overexpressed APE1, leading to the assembly of YDN into the DNA network and the fluorescence recovery of Cy5...
March 8, 2024: Nano Letters
https://read.qxmd.com/read/38456210/dna-nanospheres-assisted-spatial-confinement-signal-amplification-for-microrna-imaging-in-live-cancer-cells
#22
JOURNAL ARTICLE
Yao Wang, Li Ping Cao, Xin Jia Shuai, Lin Liu, Cheng Zhi Huang, Chun Mei Li
DNA assemblies are commonly used in biosensing, particularly for the detection and imaging of microRNAs (miRNAs), which are biomarkers associated with tumor progression. However, the difficulty lies in the exploration of high-sensitivity analytical techniques for miRNA due to its limited presence in living cells. In this study, we introduced a DNA nanosphere (DS) enhanced catalytic hairpin assembly (CHA) system for the detection and imaging of intracellular miR-21. The single-stranded DNA with four palindromic portions and extending sequences at the terminal was annealed for assembling DS, which avoided the complex sequence design and high cost of long DNA strands...
March 8, 2024: Analytical Chemistry
https://read.qxmd.com/read/38451469/integration-of-demethylation-activated-dnazyme-with-a-single-quantum-dot-nanosensor-for-sensitive-detection-of-o-6-methylguanine-dna-methyltransferase-in-breast-tissues
#23
JOURNAL ARTICLE
Yun Han, Dong-Ling Li, Qian Han, Fei Ma, Chun-Yang Zhang
O6 -Methylguanine-DNA-methyltransferase (MGMT) is a demethylation protein that dynamically regulates the O6 -methylguanine modification (O6 MeG), and dysregulated MGMT is implicated in various malignant tumors. Herein, we integrate demethylation-activated DNAzyme with a single quantum dot nanosensor to sensitively detect MGMT in breast tissues. The presence of MGMT induces the demethylation of the O6 MeG-caged DNAzyme and the restoration of catalytic activity. The activated DNAzyme then specifically cleaves the ribonucleic acid site of hairpin DNA to expose toehold sequences...
March 7, 2024: Analytical Chemistry
https://read.qxmd.com/read/38451210/an-osteoinductive-surface-by-adhesive-bone-morphogenetic-protein-2-prepared-using-the-bioorthogonal-approach-for-tight-binding-of-titanium-with-bone
#24
JOURNAL ARTICLE
Xueli Ren, Hironori Tsuji, Takahiko Uchino, Izumi Kono, Takashi Isoshima, Akimitsu Okamoto, Noriyuki Nagaoka, Toshifumi Ozaki, Akihiro Matsukawa, Hideyuki Miyatake, Yoshihiro Ito
Inorganic biomaterials are used in various orthopedic and dental implants. Nevertheless, they cause clinical issues such as loosening of implants and patient morbidity. Therefore, inspired by mussel adhesive proteins, we aimed to design an adhesive and dimer-forming highly active bone morphogenetic protein-2 (BMP-2) using bioorthogonal chemistry, in which recombinant DNA technology was combined with enzymatic modifications, to achieve long-term osseointegration with titanium. The prepared BMP-2 exhibited substantially higher binding activity than wild-type BMP-2, while the adhered BMP-2 was more active than soluble BMP-2...
March 7, 2024: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://read.qxmd.com/read/38444346/dna-nanostructures-for-exploring-cell-cell-communication
#25
REVIEW
Ya Wang, Yamin Xiong, Kangqi Shi, Clement Yaw Effah, Lulu Song, Leiliang He, Jianbo Liu
The process of coordinating between the same or multiple types of cells to jointly execute various instructions in a controlled and carefully regulated environment is a very appealing field. In order to provide clearer insight into the role of cell-cell interactions and the cellular communication of this process in their local communities, several interdisciplinary approaches have been employed to enhance the core understanding of this phenomenon. DNA nanostructures have emerged in recent years as one of the most promising tools in exploring cell-cell communication and interactions due to their programmability and addressability...
March 6, 2024: Chemical Society Reviews
https://read.qxmd.com/read/38443394/topological-barrier-to-cas12a-activation-by-circular-dna-nanostructures-facilitates-autocatalysis-and-transforms-dna-rna-sensing
#26
JOURNAL ARTICLE
Fei Deng, Yi Li, Biyao Yang, Rui Sang, Wei Deng, Maya Kansara, Frank Lin, Subotheni Thavaneswaran, David M Thomas, Ewa M Goldys
Control of CRISPR/Cas12a trans-cleavage is crucial for biosensor development. Here, we show that small circular DNA nanostructures which partially match guide RNA sequences only minimally activate Cas12a ribonucleoproteins. However, linearizing these structures restores activation. Building on this finding, an Autocatalytic Cas12a Circular DNA Amplification Reaction (AutoCAR) system is established which allows a single nucleic acid target to activate multiple ribonucleoproteins, and greatly increases the achievable reporter cleavage rates per target...
March 5, 2024: Nature Communications
https://read.qxmd.com/read/38442680/a-simple-and-reliable-interenzyme-distance-regulation-strategy-based-on-a-dna-quadrangular-prism-scaffold-for-ultrasensitive-ochratoxin-a-detection
#27
JOURNAL ARTICLE
Rong Wang, Lingqi Kong, Ying Liu, Yaqin Chai, Ruo Yuan
Developing sensitive and accurate Ochratoxin A (OTA) detection methods is essential for food safety. Herein, a simple and reliable strategy for regulating interenzyme distance based on a rigid DNA quadrangular prism as a scaffold was proposed to establish a new electrochemical biosensor for ultrasensitive detection of OTA. The interenzyme distances were precisely adjusted by changing the sequences of the hybridized portions of hairpins SH1 and SH2 to the DNA quadrangular prism, avoiding the complexity and instability of the previous DNA scaffold-based enzyme spacing adjustment strategies...
February 27, 2024: Food Chemistry
https://read.qxmd.com/read/38441369/deformable-smart-dna-nanomachine-for-synergistic-intracellular-cancer-related-mirnas-imaging-and-chemo-gene-therapy-of-drug-resistant-tumors
#28
JOURNAL ARTICLE
Chen Dong, Yeran Wang, Zhilong Chen, Chenlong Yan, Jingjing Zhang, Chunyuan Song, Lianhui Wang
Diagnosis and treatment of tumor especially drug-resistant tumor remains a huge challenge, which requires intelligent nanomedicines with low toxic side effects and high efficacy. Herein, deformable smart DNA nanomachines are developed for synergistic intracellular cancer-related miRNAs imaging and chemo-gene therapy of drug-resistant tumors. The tetrahedral DNA framework (MA-TDNA) with fluorescence quenched component and five antennas is self-assembled first, and then DOX molecules are loaded on the MA-TDNAs followed by linking MUC1-aptamer and Mcl-1 siRNA to the antennas of MA-TDNA, so that the apt-MA-TDNA@DOX-siRNA (DNA nanomachines) is constructed...
March 5, 2024: Small
https://read.qxmd.com/read/38437525/enzymatic-assembly-of-small-synthetic-genes-with-repetitive-elements
#29
JOURNAL ARTICLE
Michael T A Nguyen, Martin Vincent Gobry, Néstor Sampedro Vallina, Georgios Pothoulakis, Ebbe Sloth Andersen
Gene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences, which results in synthesis failure or delays by DNA synthesis vendors. This represents a major obstacle for the development of synthetic biology since repetitive elements are increasingly being used in the design of genetic circuits and design of biomolecular nanostructures. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is split in silico into small synthons of up to 80 base pairs flanked by Golden-Gate-compatible overhangs...
March 4, 2024: ACS Synthetic Biology
https://read.qxmd.com/read/38431928/securing-lytac-with-logic-identification-system-for-cancer-cell-selective-membrane-protein-degradation
#30
JOURNAL ARTICLE
Yanyun Fang, Yue Zhang, Shiyi Bi, Bo Peng, Caixia Wang, Huangxian Ju, Ying Liu
Lysosome-targeting chimera (LYTAC) links proteins of interest (POIs) with lysosome-targeting receptors (LTRs) to achieve membrane protein degradation, which is becoming a promising therapeutic modality. However, cancer cell-selective membrane protein degradation remains a big challenge considering expressions of POIs in both cancer cells and normal cells, as well as broad tissue distribution of LTRs. Here a logic-identification system is designed, termed Logic-TAC, based on cell membrane-guided DNA calculations to secure LYTAC selectively for cancer cells...
March 3, 2024: Small
https://read.qxmd.com/read/38431675/long-term-monitoring-of-ultratrace-nucleic-acids-using-tetrahedral-nanostructure-based-ngago-on-wearable-microneedles
#31
JOURNAL ARTICLE
Bin Yang, Haonan Wang, Jilie Kong, Xueen Fang
Real-time and continuous monitoring of nucleic acid biomarkers with wearable devices holds potential for personal health management, especially in the context of pandemic surveillance or intensive care unit disease. However, achieving high sensitivity and long-term stability remains challenging. Here, we report a tetrahedral nanostructure-based Natronobacterium gregoryi Argonaute (NgAgo) for long-term stable monitoring of ultratrace unamplified nucleic acids (cell-free DNAs and RNAs) in vivo for sepsis on wearable device...
March 2, 2024: Nature Communications
https://read.qxmd.com/read/38431020/dna-polyhedrons-cube-prism-and-square-pyramid-protect-the-catalytic-activity-of-catalase-a-thermodynamics-and-kinetics-study
#32
JOURNAL ARTICLE
Kajal Sundaray, Bineeth Baral, Umakanta Subudhi
DNA is widely used as building block material for the construction of polyhedral nanostructures. DNA polyhedrons (DNA prism, cube, and square pyramid) are small 3D wireframed nanostructures with tunable shapes and sizes. Despite substantial progress in synthesis, the study regarding cellular responses to DNA polyhedrons is limited. Herein, the molecular interaction between DNA polyhedrons and the antioxidant enzyme, catalase has been explored. The enzymatic activity of bovine liver catalase (BLC) remains unaltered in the presence of DNA polyhedrons after 1 h of incubation...
February 29, 2024: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38426244/bimodal-effects-on-lipid-droplets-induced-in-cancer-and-non-cancer-cells-by-chemotherapy-drugs-as-revealed-with-a-green-emitting-bodipy-fluorescent-probe
#33
JOURNAL ARTICLE
Artūras Polita, Rokas Žvirblis, Jelena Dodonova-Vaitkūnienė, Arun Prabha Shivabalan, Karolina Maleckaitė, Gintaras Valinčius
Lipid droplets (LDs) are cytoplasmic lipid-rich organelles with important roles in lipid storage and metabolism, cell signaling and membrane biosynthesis. Additionally, multiple diseases, such as obesity, fatty liver, cardiovascular diseases and cancer, are related to the metabolic disorders of LDs. In various cancer cells, LD accumulation is associated with resistance to cell death, reduced effectiveness of chemotherapeutic drugs, and increased proliferation and aggressiveness. In this work, we present a new viscosity-sensitive, green-emitting BODIPY probe capable of distinguishing between ordered and disordered lipid phases and selectively internalising into LDs of live cells...
March 1, 2024: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://read.qxmd.com/read/38417645/bacterial-extracellular-vesicles-modulation-of-biofilm-formation-and-virulence
#34
REVIEW
Geum-Jae Jeong, Fazlurrahman Khan, Nazia Tabassum, Kyung-Jin Cho, Young-Mog Kim
Microbial pathogens cause persistent infections by forming biofilms and producing numerous virulence factors. Bacterial extracellular vesicles (BEVs) are nanostructures produced by various bacterial species vital for molecular transport. BEVs include various components, including lipids (glycolipids, LPS, and phospholipids), nucleic acids (genomic DNA, plasmids, and short RNA), proteins (membrane proteins, enzymes, and toxins), and quorum-sensing signaling molecules. BEVs play a major role in forming extracellular polymeric substances (EPS) in biofilms by transporting EPS components such as extracellular polysaccharides, proteins, and extracellular DNA...
February 26, 2024: Acta Biomaterialia
https://read.qxmd.com/read/38414318/effects-of-tetrahedral-dna-nanostructures-on-the-treatment-of-osteoporosis
#35
JOURNAL ARTICLE
Weitong Cui, Xiao Yang, Yikai Dou, Yue Du, Xiaohong Ma, Lei Hu, Yunfeng Lin
Osteoporosis (OP) is a common disease characterized by bone loss and bone tissue microstructure degradation. Drug treatment is a common clinical treatment that aims to increase bone mass and bone density. Tetrahedral DNA nanostructures (TDNs) are three-dimensional tetrahedral frames formed by folding four single-stranded DNA molecules, which have good biological safety and can promote bone regeneration. In this study, a mouse model of OP was established by ovariectomy (OVX) and TDN was injected into the tail vein for 8 weeks...
February 27, 2024: Cell Proliferation
https://read.qxmd.com/read/38412242/fluorophore-label-free-light-up-near-infrared-deoxyribonucleic-acid-nanosensor-for-monitoring-extracellular-potassium-levels
#36
JOURNAL ARTICLE
Zhiwei Deng, Jiacheng Ding, Jiaqi Bu, Jiacheng Li, Hui Liu, Peiru Gao, Zan Gong, Xiangxiang Qin, Yanjing Yang, Shian Zhong
Fluorescent DNA nanosensors have been widely used due to their unique advantages, among which the near-infrared (NIR) imaging mode can provide deeper penetration depth and lower biological background for the nanosensors. However, efficient NIR quenchers require ingenious design, complex synthesis, and modification, which severely limit the development of NIR DNA nanosensors. Label-free strategies based on G-quadruplex (G4) and NIR G4 dyes were first introduced into in situ extracellular imaging, and a novel NIR sensing strategy for the specific detection of extracellular targets is proposed...
February 27, 2024: Analytical Chemistry
https://read.qxmd.com/read/38411498/framework-nucleic-acids-as-promising-reactive-oxygen-species-scavengers-for-anti-inflammatory-therapy
#37
REVIEW
Yujie Zhu, Ruijianghan Shi, Weitong Lu, Sirong Shi, Yang Chen
Reactive oxygen species (ROS) are an array of derivatives of molecular oxygen that participate in multiple physiological processes under the control of redox homeostasis. However, under pathological conditions, the over-production of ROS often leads to oxidative stress and inflammatory reactions, indicating a potential therapeutic target. With the rapid development of nucleic acid nanotechnology, scientists have exploited various DNA nanostructures with remarkable biocompatibility, programmability, and structural stability...
February 27, 2024: Nanoscale
https://read.qxmd.com/read/38408974/highly-sensitive-sers-platform-for-pathogen-analysis-by-cyclic-dna-nanostructure-aunp-tags-and-cascade-primer-exchange-reaction
#38
JOURNAL ARTICLE
Yunju Xiao, Shihua Luo, Jiuxiang Qiu, Ye Zhang, Weijiang Liu, Yunhu Zhao, YiTong Zhu, Yangxi Deng, Mengdi Lu, Suling Liu, Yong Lin, Aiwei Huang, Wen Wang, Xuejiao Hu, Bing Gu
The capacity to identify small amounts of pathogens in real samples is extremely useful. Herein, we proposed a sensitive platform for detecting pathogens using cyclic DNA nanostructure@AuNP tags (CDNA) and a cascade primer exchange reaction (cPER). This platform employs wheat germ agglutinin-modified Fe3 O4 @Au magnetic nanoparticles (WMRs) to bind the E. coli O157:H7, and then triggers the cPER to generate branched DNA products for CDNA tag hybridization with high stability and amplified SERS signals. It can identify target pathogens as low as 1...
February 26, 2024: Journal of Nanobiotechnology
https://read.qxmd.com/read/38408644/dna-digestion-and-formation-of-dna-network-structures-with-holliday-junction-resolving-enzyme-hjc_15-6-in-conjunction-with-polymerase-reactions
#39
JOURNAL ARTICLE
Josefin Ahlqvist, Joanna Tymecka-Mulik, Katarzyna Burkiewicz, Andrius Jasilionis, Reine Wallenberg, Eva Nordberg Karlsson, Slawomir Dabrowski
The recently identified novel Holliday junction-resolving enzyme, termed Hjc_15-6, activity investigation results imply DNA cleavage by Hjc_15-6 in a manner that potentially enhances the molecular self-assembly that may be exploited for creating DNA-networks and nanostructures. The study also demonstrates Pwo DNA polymerase acting in combination with Hjc_15-6 capability to produce large amounts of DNA that transforms into large DNA-network structures even without DNA template and primers. Furthermore, it is demonstrated that Hjc_15-6 prefers Holliday junction oligonucleotides as compared to Y-shaped oligonucleotides as well as efficiently cleaves typical branched products from isothermal DNA amplification of both linear and circular DNA templates amplified by phi29-like DNA polymerase...
February 24, 2024: Journal of Biotechnology
https://read.qxmd.com/read/38406926/crispr-cas-systems-combined-with-dna-nanostructures-for-biomedical-applications
#40
REVIEW
Shujuan Sun, Haoqi Yang, Ziyong Wu, Shusheng Zhang, Jingjuan Xu, Pengfei Shi
DNA nanostructures are easy to design and construct, have good biocompatibility, and show great potential in biosensing and drug delivery. Numerous distinctive and versatile DNA nanostructures have been developed and explored for biomedical applications. In addition to DNA nanostructures that are completely assembled from DNA, composite DNA nanostructures obtained by combining DNA with other organic or inorganic materials are also widely used in related research. The CRISPR/Cas system has attracted great attention as a powerful gene editing technology and is also widely used in biomedical diagnosis...
March 14, 2024: Chemical Communications: Chem Comm
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