Article
Chemistry, Analytical
Zhe Dong, Debo Gao, Yuancheng Li, Kang An, Jing Ni, Ling Meng, Han Wu
Summary: This study develops DNA nanoparticles with GSH-responsive controllable release of hairpin reactants for the analysis and imaging of low-abundance target mRNA in living cells. The DNA nanoparticles exhibit stability, cell-specific penetration, and precise controllability. By combining multi-amplifiers and programmable DNA nanostructures, the strategy enables accurately triggered release of hairpin reactants, achieving sensitive imaging and quantitative evaluation of survivin mRNA in carcinoma cells.
ANALYTICA CHIMICA ACTA
(2023)
Article
Chemistry, Analytical
Jinjoo Han, Seokhwan Kim, Seokjoon Kim, Eun Sung Lee, Byung Seok Cha, Jung Soo Park, Jiye Shin, Youngjun Jang, Ki Soo Park
Summary: In this study, a strategy using Cas12a protein for active primer production and subsequent isothermal amplification was proposed. The target nucleic acids activated Cas12a to cleave inactive RNA-DNA chimera primers into active ones. Two isothermal amplification methods generated fluorescence and colorimetric signals, allowing effective detection of the Sal-monella enterotoxin gene even in real samples such as drinking water and human serum.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Analytical
Liu Yang, Jie Fang, Junjie Li, Xinying Ou, Li Zhang, Yufeng Wang, Zhi Weng, Guoming Xie
Summary: In this study, a fluorescent microRNA biosensor based on EXPAR and BDW was designed, utilizing enzyme-assisted amplification in solution and enzyme-powered BDW on particles to enhance signal amplification efficiency and improve detection sensitivity. The method has a wide linear range and low detection limit, showing potential for BDW-related biosensor applications.
ANALYTICA CHIMICA ACTA
(2021)
Article
Nanoscience & Nanotechnology
Marta Broto, Michael M. Kaminski, Christopher Adrianus, Nayoung Kim, Robert Greensmith, Schan Dissanayake-Perera, Alexander J. Schubert, Xiao Tan, Hyemin Kim, Anand S. Dighe, James J. Collins, Molly M. Stevens
Summary: This study combines CRISPR-Cas reaction with nanozyme-linked ELISA to achieve quantitative detection of Cas13-mediated RNA detection through catalytic metallic nanoparticles at room temperature (CrisprZyme). The study shows that CrisprZyme is adaptable to lateral flow reading and different Cas enzymes, and can detect various non-coding RNAs. The platform can be used to identify disease patients and monitor cellular differentiation. CrisprZyme can serve as a universally applicable signal catalyst for CRISPR-based diagnostics, expanding the target range of preamplification-free, quantitative detection.
NATURE NANOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Joakim Bohlin, Michael Matthies, Erik Poppleton, Jonah Procyk, Aatmik Mallya, Hao Yan, Petr Sulc
Summary: Molecular simulation is essential in DNA/RNA nanotechnology research, improving the precision of nanoscaffolds and diagnostic tools. oxView is a design tool for visualizing, designing, editing, and analyzing simulations of DNA, RNA, and nucleic acid-protein nanostructures, providing an accessible software platform for researchers to integrate simulation and 3D visualization into their projects.
Article
Biophysics
Yuanyuan Zhu, Jian Wu, Qingli Zhou
Summary: Functional DNA (fDNA) refers to DNA molecules that have specific binding ability or catalytic function, with advantages of simple synthesis, low cost, low toxicity, high chemical stability, recognition specificity, and biocompatibility. However, the limited sensitivity of fDNA sensors to trace targets is a major challenge, especially when there is low affinity between fDNA and the targets. Various nucleic acid signal amplification strategies (NASAS) have been explored to improve the limit of detection of fDNA. This review summarizes four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and their corresponding design principles, as well as the principle and application of fDNA sensors integrated with signal amplification strategies for the detection of non-nucleic acid targets. The main challenges and application prospects of NASAS-integrated fDNA biosensing system are also discussed.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Analytical
Mahera J. Kachwala, Christopher W. Smith, Nidhi Nandu, Mehmet Yigit
Summary: Hybridization chain reaction (HCR) is a DNA-based target-induced cascade reaction that is often used for sensing applications due to its unique enzyme-free amplification feature. HCR is highly modular and can be advanced and repurposed when coupled with latest discoveries for improved sensitivity and programmability. Incorporating CRISPR-Cas12a into HCR can enhance sensitivity and enable rapid reprogramming of detection assays, making it more versatile for detecting different target sequences.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Yong Chen, Yibin Zhang, Siyuan Luo, Xinyao Yang, Conghui Liu, Qianling Zhang, Yizhen Liu, Xueji Zhang
Summary: This study presents a foldback-crRNA-enhanced CRISPR/Cas13a (FCECas13a) system that overcomes the limitations of conventional CRISPR/Cas13a system in detecting ultrashort sncRNAs. The FCECas13a system utilizes a 3'-terminal foldback crRNA that forms a double strand with the target ultrashort sncRNA, activating the Cas13a nuclease and achieving accurate detection.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Tong Luo, Jiacheng Li, Yao He, Hui Liu, Zhiwei Deng, Xi Long, Qingqing Wan, Jiacheng Ding, Zan Gong, Yanjing Yang, Shian Zhong
Summary: In this study, we developed a novel CRISPR-based biosensor by combining CRISPR/Cas12a with Au-nanobeacon, which allows for direct and rapid detection of nucleic acids in complex biological fluids with high sensitivity.
ANALYTICAL CHEMISTRY
(2022)
Article
Microbiology
Montserrat Nacher-Vazquez, Bruno Santos, Nuno Filipe Azevedo, Laura Cerqueira
Summary: Fluorescent in situ hybridization (FISH) is a powerful tool for detecting and studying the spatial distribution of microorganisms. The emergence of Nucleic Acid Mimics (NAMs) has improved the FISH technique, enhancing its sensitivity, specificity, and flexibility.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Chemistry, Analytical
Masanobu Iwanaga
Summary: The global pandemic caused by SARS-CoV-2 has greatly impacted daily lives, leading to an urgent need for high-throughput nucleic acid detection methods. The high-sensitivity and high-throughput metasurface fluorescence biosensors developed in this study demonstrated excellent performance in detecting oligoDNA sequences simulating SARS-CoV-2 RNA, even at low concentrations without amplification techniques.
Article
Chemistry, Analytical
Qiuyuan Lin, Yuanwei Cao, Guobin Han, Wen Sun, Wenhao Weng, Hui Chen, Haoyi Wang, Jilie Kong
Summary: We report a general and programmable diagnostic platform that combines mesophilic Clostridium perfringens Argonaute (CpAgo) with exponential isothermal amplification (EXPAR) for the rapid and sensitive detection of multiple miRNAs with single-nucleotide discrimination in one pot. The CpAgo-based One-Pot (COP) assay achieved a limit of detection of 1 zMmiRNA within 30 min and showed superior analytical performance in distinguishing colorectal cancer patients from healthy individuals. This programmable, one-pot, multiplex, rapid, and specific strategy holds great promise in scientific research and clinical applications.
ANALYTICAL CHEMISTRY
(2023)
Review
Food Science & Technology
Tai-Yong Kim, Xiaoning Zhu, Se-Min Kim, Jeong-A Lim, Min-Cheol Lim, Ke Luo
Summary: Viruses are major pathogens in food poisoning, and the development of foodborne virus detection technologies for the entire food distribution chain is crucial for food safety. Polymerase chain reaction (PCR) is the gold standard method for monitoring food contamination by viruses, but it is time-consuming and vulnerable to inhibitors in food samples. Optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives, offering portability and on-site operation. However, the complexity of food components and lack of stability studies on residual food components limit the practical application of biosensors as a universal detection method.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Chemistry, Analytical
Peng Yang, Haoran Chen, Quanjing Zhu, Zhaopeng Chen, Zezhou Yang, Ruo Yuan, Yan Li, Wenbin Liang
Summary: This study developed a novel autocatalytic three-dimensional DNA nanomachine based on cross-catalytic hairpin assembly on gold nanoparticles, achieving self-powered efficient cyclic amplification. The strategy not only enables high-efficiency analysis of microRNAs, but also provides a new pathway for highly processive DNA nanomachines.
Article
Biochemistry & Molecular Biology
Qian Liu, Xiang Guo, Guanhua Xun, Zhonglei Li, Yuesheng Chong, Litao Yang, Hongxia Wang, Fengchun Zhang, Shukun Luo, Li Cui, Pengshu Zhao, Xingyu Ye, Heshan Xu, Hui Lu, Xiao Li, Zixin Deng, Kai Li, Yan Feng
Summary: The A-Star system, utilizing PfAgo for efficient detection of rare DNA mutations, greatly improves the enrichment efficiency of rare mutations and enables simultaneous detection of multiple oncogenes. It shows promising potential for both research and therapeutic applications in nucleic acid detection.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Polymer Science
Mahmoud H. Othman, Yoshihiro Ito, Jun Akimoto
Summary: In this study, water-soluble and highly antibiofouling polymers were synthesized and immobilized on polystyrene surfaces via photoirradiation. These polymers showed excellent solubility in water and suppressed nonspecific interactions between proteins and cells on the substrate, making them useful for biomaterial preparation.
Article
Materials Science, Biomaterials
Liang-Chun Wu, Seiichi Tada, Takashi Isoshima, Takeshi Serizawa, Yoshihiro Ito
Summary: Photo-reactive polymers are essential for biomaterials and have been employed for immobilizing growth factors. Different types of photo-reactive polymers were synthesized and their properties were analyzed. The study found that cell adhesion was influenced by the nature of photo-reactive polymers, while cell growth depended on the amount of immobilized growth factors and the properties of photo-reactive polymers.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Analytical
Ren-Qi Wang, Ye Geng, Juan-Na Song, Huai-Dong Yu, Kai Bao, Yu-Ru Wang, Jean-Philippe Croue, Hideyuki Miyatake, Yoshihiro Ito, Yan-Ru Liu, Yong-Mei Chen
Summary: This study develops a biogenic solution map based on a 4D fingerprinting method to accurately discriminate and classify unknown species. It allows visualization of the similarities and disparities in molecular compositions of biogenic solutions, as well as the intrinsic correlations and subtle variations among them.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Fumitaka Hashiya, Hirotaka Murase, Akash Chandela, Haruka Hiraoka, Masahito Inagaki, Yuko Nakashima, Naoko Abe, Mayu Nakamura, Goro Terai, Yasuaki Kimura, Kaori Ando, Natsuhisa Oka, Kiyoshi Asai, Hiroshi Abe
Summary: Controlling PCR fidelity is crucial in molecular biology, and high-fidelity PCR is essential for gene cloning. While most studies focus on protein engineering of polymerases for fidelity control, this report explores the use of chemically modified nucleotide substrates. The modification on P-gamma of nucleotide substrates was found to affect PCR fidelity, with deoxyadenosine tetraphosphate enhancing one mutation type and deoxyguanosine tetraphosphate suppressing another. By using excess amounts of deoxyguanosine tetraphosphate, both mutations were successfully suppressed, leading to improved overall fidelity.
Article
Multidisciplinary Sciences
Masahito Inagaki, Naoko Abe, Zhenmin Li, Yuko Nakashima, Susit Acharyya, Kazuya Ogawa, Daisuke Kawaguchi, Haruka Hiraoka, Ayaka Banno, Zheyu Meng, Mizuki Tada, Tatsuma Ishida, Pingxue Lyu, Kengo Kokubo, Hirotaka Murase, Fumitaka Hashiya, Yasuaki Kimura, Satoshi Uchida, Hiroshi Abe
Summary: Starting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for various applications. Removing uncapped mRNA is important in mRNA research and clinical applications. This study developed a method to separate capped mRNA from uncapped mRNA using hydrophobic photocaged tag-modified cap analogs, achieving 100% capping efficiency. It was found that the Cap-2-type mRNA showed higher translational activity compared to the Cap-1-type mRNA prepared by the standard capping method.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Osama R. M. Metawea, Miyuki Nara, Takeharu Murakami, Satoshi Wada, Katsushi Fujii, Yoshihiro Ito, Masuki Kawamoto
Summary: A highly efficient single-walled carbon nanotube electrocatalyst, loaded with platinum nanoparticles using a newly developed suspension method, exhibits low overpotential for hydrogen evolution and shows high mass activity in a PEM electrolyzer.
ADVANCED MATERIALS INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Jyorthana Rajappa Muralidhar, Krishnachary Salikolimi, Kiyohiro Adachi, Daisuke Hashizume, Koichi Kodama, Takuji Hirose, Yoshihiro Ito, Masuki Kawamoto
Summary: We report an organic-inorganic halide perovskite compound that can chemically store ammonia through dynamic structural transformation. This compound undergoes a chemical structure change from a one-dimensional columnar structure to a two-dimensional layered structure upon NH3 uptake through addition reaction. The estimated NH3 uptake is 10.2 mmol g(-1) at 1 bar and 25℃. NH3 extraction can be performed by a condensation reaction at 50℃ under vacuum. X-ray diffraction analysis reveals that reversible NH3 uptake/extraction originates from a cation/anion exchange reaction. These findings demonstrate the potential of integrating efficient uptake and extraction in a hybrid perovskite compound through chemical reaction, paving the way for further exploration of dynamic and reversible compounds for chemical storage of NH3.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Nanoscience & Nanotechnology
Osama R. M. Metawea, Miyuki Nara, Takeharu Murakami, Hirotaka Okabe, Naoki Matsuda, Satoshi Wada, Katsushi Fujii, Yoshihiro Ito, Masuki Kawamoto
Summary: Proton exchange membrane (PEM) water electrolysis is a promising method for clean hydrogen production. A new approach using aqueous-dispersed PtNPs as a dispersant for carbon nanomaterials (CNMs) is reported, resulting in efficient PtNP/CNM composites. The PtNP/SWCNT nanocomposite exhibits a mass activity of 89,300 A g(Pt) (-1), 270 times higher than that of Pt/C.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Avanashiappan Nandakumar, Yoshihiro Ito, Motoki Ueda
Summary: A disulfide-tethered peptide-lipid conjugate can self-assemble into a homogeneously distributed peptide-lipid hybrid vesicle. Treatment with dithiothreitol causes the homogeneous peptide-lipid membrane to spontaneously separate into lipid-rich and peptide-rich domains, while the vesicle remains unchanged in size and shape. Membrane phase separation enhances temperature-dependent cargo release.
CHEMICAL COMMUNICATIONS
(2023)
Article
Materials Science, Biomaterials
Mohamed S. S. Elafify, Toru Itagaki, Nermeen A. A. Elkasabgy, Sinar Sayed, Yoshihiro Ito, Motoki Ueda
Summary: The development of stimuli-responsive transformable biomaterials can be effectively controlled by adjusting the molecular design of their structural segments. In this study, we demonstrate a peptide assembly that exhibits morphological transformations between hydrophilic and hydrophobic morphologies. The hydrophobic α-helical unit precisely controls the packing and induces the formation of tubules in the assembly. By analyzing membrane fluidity and the surrounding environment of the assembly, we clarify that the vesicle is kinetically stable while the nanotube is thermodynamically stable.
BIOMATERIALS SCIENCE
(2023)
Article
Materials Science, Biomaterials
Kun Fang, Stefan Muller, Motoki Ueda, Yasuhiro Nakagawa, Katsuko Furukawa, Takashi Ushida, Toshiyuki Ikoma, Yoshihiro Ito
Summary: Fibroblasts confined by gelatin micropatterns and subjected to cyclic stretch showed significant changes in cell morphology. Non-patterned cells exhibited increasing length and decreasing area under the stretch. The width of the micropatterns provided different contact guidance for fibroblasts, resulting in varied cell behaviors under cyclic stretch. Vertical stretch induced a greater increase in cell area and length compared to parallel stretch. These findings provide insights into cell behaviors under geometrical confinement in a dynamic biomechanical environment and can guide biomaterial design for tissue engineering.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Review
Materials Science, Biomaterials
Xiaoyu Guan, Bingyuan Zhang, Zequn Wang, Qingxin Han, Meng An, Motoki Ueda, Yoshihiro Ito
Summary: Tannins, natural plant polyphenols, are widely used in various fields, especially in biomedical applications. However, their water solubility limits their use in specific applications, making separation and regeneration difficult. Tannin-immobilized composites, inspired by composite materials, combine the advantages of each component, allowing for expanded applications in different fields.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Organic
Shogo Hasegawa, Masahito Inagaki, Shunichi Kato, Zhenmin Li, Yasuaki Kimura, Hiroshi Abe
Summary: We present a novel approach for synthesizing nucleoside oligophosphates by electrophilic activation of 5'-phosphorothioate nucleotides. Treatment of phosphorothioate with 2,4-dinitrochlorobenzene (DNCB) efficiently produced electrophilic thioester nucleotides (EPT-Ns), which were then coupled with various phosphate reagents to yield the desired nucleoside oligophosphates, including an mRNA cap analog.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Toshinobu Nakajo, Shinpei Kusaka, Haruka Hiraoka, Kohei Nomura, Noriaki Matsubara, Rintaro Baba, Yuki Yoshida, Kosuke Nakamoto, Masakazu Honma, Hiroaki Iguchi, Takayuki Uchihashi, Hiroshi Abe, Ryotaro Matsuda
Summary: We developed an equimolar conjugate of a metal-organic cage (MOC) and DNA (MOC-DNA). By coordinating with a template DNA, several MOC-DNA conjugates were assembled into a programmed structure. Additionally, the conjugation with MOC greatly enhanced the permeability of DNA through lipid bilayer, showing promising potential as a drug delivery system.
CHEMICAL COMMUNICATIONS
(2023)
Article
Pharmacology & Pharmacy
Rabab A. Husseini, Naoko Abe, Tomoaki Hara, Hiroshi Abe, Kentaro Kogure
Summary: This study demonstrates the use of iontophoresis for the delivery of a minimal mRNA vaccine, which activates skin resident immune cells and induces tumor clearance, showing potential for melanoma therapy.
BIOLOGICAL & PHARMACEUTICAL BULLETIN
(2023)
