Article
Chemistry, Analytical
Biao Chen, Wenjie Ma, Xu Long, Hong Cheng, Huanhuan Sun, Jin Huang, Ruichen Jia, Xiaoxiao He, Kemin Wang
Summary: This research report presents a membrane protein and extracellular acid heterogeneity-driven amplified DNA logic gate (HDLG) for accurate and sensitive identification of cancer cells. The HDLG combines the signal amplification characteristics of the hybridization chain reaction (HCR) and the precise computation ability of the logic operation.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Applied
Hongyi Zhang, Qikai Ju, Shude Pang, Ningning Wei, Yanru Zhang
Summary: This paper discusses the distribution of alkaline phosphatase (ALP) in the human body and its association with other diseases, as well as the application of fluorescent probes in detecting ALP activity and imaging.
Review
Chemistry, Analytical
Kai Wang, Wei Wang, Xiang-Yang Zhang, Ai-Qin Jiang, Yu-Shun Yang, Hai-Liang Zhu
Summary: This review summarizes the characteristics and research progress of ALP fluorescent probes, introduces the importance of ALP in physiological and pathological events, and highlights the advantages of fluorescent probes in ALP detection, providing an important reference for related research.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Karim Widad Temgbet Nchourupouo, Jules Nde, Yannick Joel Wadop Ngouongo, Serge Sylvain Zekeng, Bernard Fongang
Summary: A growing body of evidence suggests that only a few hot-spot amino acids at the interface contribute most of the binding energy in transient protein-protein interactions. Experimental protocols to identify these hot-spots are labor-intensive and expensive. Computational methods using evolutionary couplings followed by biased molecular dynamic simulations were shown to successfully predict the binding interfaces of G-protein coupled receptors and reveal the critical residues of protein complexes.
Review
Chemistry, Multidisciplinary
Chi Yao, Junhan Ou, Jianpu Tang, Dayong Yang
Summary: Facing the increasing demand for precision medicine, materials chemistry systems with accurate molecular design, controllable structure, and adjustable biological activity are required for bioanalysis. In recent years, DNA has been considered a potential biomaterial for analysis and has been applied in various fields. DNA supramolecular assembly on micro/nanointerfaces is an effective strategy to concentrate functional DNA modules and enhance their functions in bioanalysis. This research direction is expected to guide the construction of more bioanalytical materials and promote the development of precision medicine.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Yangyang Chang, Qian Zhang, Wei Xue, Yanfang Wu, Yi Liu, Meng Liu
Summary: We developed a paper-based analytical device that utilizes 3D DNA encapsulating horseradish peroxidase (HRP) for detecting alkaline phosphatase (ALP) visually. This device allows for on-paper sample pre-treatment, target recognition, and signal readout, enabling simple and rapid determination of ALP in clinical samples without the need for additional blood sample pre-treatment (within 23 minutes).
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Fan Xu, Baijun Dong, Xue Li, Fei Gao, Donglei Yang, Wei Xue, Pengfei Wang
Summary: This study conducted proteomic analysis to profile proteins that bind to DNA materials in human serum, revealing distinctive protein profiles for each DNA material and significant differences in profiles when serum originates from healthy donors vs prostate cancer patients. Furthermore, tethering single-stranded DNA onto DNA material can regulate protein profiles and improve biological performance.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Dian Li, Ying Liu, Shengrong Yu, Dailiang Zhang, Xiao Wang, Hongmei Zhong, Kangdi He, Ying Wang, Yong-Xiang Wu
Summary: A novel nanoprobe platform with two-photon dye-doped silica nanoparticles was developed for FRET-based ratiometric biosensing and bioimaging targeting endogenous ATP. The nanoprobe showed satisfactory ratiometric fluorescence responses for ATP detection with high sensitivity and selectivity in vivo, indicating its potential as a valuable molecular imaging tool for biomedical applications.
Article
Biochemistry & Molecular Biology
Yolanda Alacid, Maria Jose Martinez-Tome, Rocio Esquembre, M. Antonia Herrero, C. Reyes Mateo
Summary: In this study, alkaline phosphatase (ALP) was incorporated into a three-dimensional polymeric network through a green protocol to obtain transparent hydrogels (ALP@AETA). The immobilized enzyme retained its activity, slightly increased its thermal stability, and could be stored as a xerogel at room temperature. The ALP@AETA xerogel showed promise as a disposable biosensor for detecting ALP inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Kaori Tsukakoshi, Rikako Kubo, Kazunori Ikebukuro
Summary: In this study, a fusion protein called PrP-ALP was developed as a sensing element to detect toxic A beta oligomers. PrP-ALP showed strong affinity towards high molecular weight oligomers and has potential for detecting A beta oligomers. This study is important for understanding the pathogenesis of Alzheimer's disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Yulin Du, Yifan Lyu, Shiquan Li, Ding Ding, Jianghuai Chen, Cai Yang, Yang Sun, Fengli Qu, Zeyu Xiao, Jianhui Jiang, Weihong Tan
Summary: Cell-specific aptamers are a strong tool for studying membrane receptors at the single-molecule level. Ligand dilution analysis (LDA) is proposed as a random sampling-based strategy to study aptamer-based receptors. This strategy allows for the calculation of receptor density, colocalization and differentiation of aptamer and monoclonal antibody binding, and determination of binding site and aptamer-receptor binding mode.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Nanoscience & Nanotechnology
Ling Sum Liu, Fei Wang, Yonghe Ge, Pik Kwan Lo
Summary: This paper explores the diverse applications of aptamers in biosensors, focusing on their binding configurations and signal transduction strategies. Researchers are interested in the potential of aptamers for clinical diagnosis, aiming to enhance sensitivity and detection limits of target determination.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Review
Chemistry, Multidisciplinary
Meng Li, Bhaskar Gurram, Shan Lei, Nicholas T. Blum, Peng Huang, Jing Lin
Summary: Phosphatase is crucial in many biological functions, with alkaline phosphatase (ALP) serving as a key prognostic indicator for various diseases, though current detection methods are limited to in vitro colorimetric techniques. Fluorescence imaging provides a reliable way to monitor real-time changes in ALP levels, with research focusing mainly on ALP imaging probes grouped by their luminescence mechanisms. Challenges and future prospects for phosphatase probes were also discussed.
CHINESE CHEMICAL LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Yilmaz Yucehan Yazici, Serkan Belkaya, Emel Timucin
Summary: IL18 is a pro-inflammatory cytokine that regulates immune responses. The activity of IL18 is controlled by IL18BP. The structure and dynamics of the IL18-IL18BP heterodimers are affected by a short surface epitope between amino acids 68 and 81. MD simulations showed that the helical form of this epitope stabilizes the complex and contributes to IL18-IL18BP stability.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Shi Xuan Leong, Ya-Chuan Kao, Xuemei Han, Zhong Wei Poh, Jaslyn Ru Ting Chen, Emily Xi Tan, Yong Xiang Leong, Yih Hong Lee, Wei Xuan Teo, George W. Yip, Yulin Lam, Xing Yi Ling
Summary: This study demonstrates the use of charge and geometry complementarity to achieve high spectral specificity in surface-enhanced Raman scattering (SERS) molecular recognition. By leveraging this approach, accurate differentiation and quantification of structurally similar biomolecules can be achieved, which holds significance in fields such as biodiagnostics, food, and environmental surveillance.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Spectroscopy
Lingling Zhang, Mengwen Yi, Shilong Zhong, Jing Liu, Xiangjun Liu, Tao Bing, Nan Zhang, Yongbiao Wei, Dihua Shangguan
Summary: The viscosity of the cell microenvironment is crucial for maintaining normal cellular activities, with abnormal viscosity in mitochondria linked to various diseases. Novel p-aminostyryl thiazole orange derivatives have been developed, showing good fluorescence response to viscosity and potential for monitoring mitochondrial viscosity changes and investigating physiological processes related to inflammation and lipid metabolism.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Medicine, Research & Experimental
Nan Zhang, Junyan Wang, Tao Bing, Xiangjun Liu, Dihua Shangguan
Summary: Aptamers have high specificity and affinity in targeting cell surface receptors, making them promising for targeted drug delivery. Understanding the receptor-mediated internalization process of aptameric conjugates can aid in designing new targeted drugs. In this study, human transferrin receptor-targeted DNA aptamer-fluorophore conjugates were used to study the internalization, intracellular transport, and environmental pH of aptameric conjugates. The results showed that the aptameric conjugates had lower recycling ratios and dissociated from receptors, suggesting they could efficiently release loaded drugs and serve as a versatile tool for specific and effective delivery of therapeutic payloads.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Chemistry, Analytical
Yue Sun, Zhicheng Zhang, Tao Bing, Jing Liu, Weiwei Li, Xiangjun Liu, Nan Zhang, Yang Shu, Jianhua Wang, Dihua Shangguan
Summary: Aptamer-based Expansion Microscopy (ExM) is a newly developed imaging technology that allows nanoscale imaging under conventional microscopes. This technique utilizes chemically labeled aptamers for molecular recognition, fluorescence reporting, and gel anchoring, enabling high-resolution imaging after gel expansion. It offers a simple and promising approach for super-resolution imaging of cells and tissues.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Tianjun Chang, Guangping Li, Zhan Ding, Weiguo Li, Panpan Zhu, Wei Lei, Dihua Shangguan
Summary: This study discovered a prevalence of putative G4-forming sequences (PQSs) in nuclease hypersensitive sites within the promoters of heat-responsive genes in rice. The study also demonstrated that these PQSs could adopt stable G4 structures at physiological temperature and exhibit structural switch in response to temperature changes.
Article
Chemistry, Analytical
Jing Lv, Xiaoxiao Zhen, Dandan Li, Guomiao Liao, Zhenhao Long, Nan Zhang, Xiangjun Liu, Tao Bing, Dihua Shangguan
Summary: Cell-SELEX is a powerful tool for generating aptamers that specifically bind to native molecules on living cells. In this study, an aptamer named ZAJ4a was generated using cell-SELEX and was shown to have high binding affinity to cancer cells expressing the receptor-type tyrosine-protein phosphatase F (PTPRF). This aptamer can potentially be used as a molecular probe to identify biomarkers on the cell surface.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
P. Delgado, O. Oshinowo, M. E. Fay, C. A. Luna, A. Dissanayaka, P. Dorbala, A. Ravindran, L. Shen, D. R. Myers
Summary: Integrating microfluidic mixers into lab-on-a-chip devices is challenging but important. The presented universal dry-film microfluidic mixing sticker can retrofit pre-existing microfluidics and maintain high performance. It utilizes laser-cut silicone-adhesive-coated polymer sheets to create complex designs that can be adhered to various surfaces, allowing easy assembly of the traditional F-mixer and a novel spiral F-mixer. The technology has numerous applications in point-of-care devices, microphysiological systems, and biomedical research.
Article
Multidisciplinary Sciences
Qian Ma, Mingzhi Zhang, Chao Zhang, Xiaoyan Teng, Linlin Yang, Yuan Tian, Junyan Wang, Da Han, Weihong Tan
Summary: Rapid and accurate classification of the etiology for acute respiratory illness is crucial for effective treatment and avoiding unnecessary antibiotic use. Researchers have developed an automated DNA computing-based platform that can accurately diagnose the cause of acute respiratory infection in just 4 hours, providing a low-cost and automated solution for emergency departments and point-of-care clinics.
Article
Biochemistry & Molecular Biology
Zhenhao Long, Tao Bing, Xiangru Zhang, Jing Sheng, Shuang Zu, Weiwei Li, Xiangjun Liu, Nan Zhang, Dihua Shangguan
Summary: The L1 cell adhesion molecule (L1CAM) plays important roles in the development and plasticity of the nervous system as well as in tumor formation, progression, and metastasis. DNA aptamers yly20 and yly21, optimized through sequence mutation and extension, exhibit much stronger binding affinity to L1CAM at both room temperature and 37 degrees C. These aptamers adopt a hairpin structure containing two loops and two stems, with key nucleotides for binding mainly located in loop I and its adjacent area. This study provides insights into the molecular mechanism of the interaction between yly-series aptamers and L1CAM, and has implications for drug development and detection probe design against L1CAM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemical Research Methods
Adiya E. Otumala, Dominick J. Hellen, C. Alessandra Luna, Priscilla Delgado, Anjana Dissanayaka, Chidozie Ugwumadu, Oluwamayokun Oshinowo, Md. Mydul Islam, Luyao Shen, Saul J. Karpen, David R. Myers
Summary: Advances in microsystem engineering have led to the development of controlled liver models that more accurately replicate in vivo conditions. Progress has been made in creating complex liver models that mimic key metabolic, structural, and oxygen gradients. This review discusses the current state of liver-centric microphysiological systems and the potential for investigating liver diseases and therapeutic challenges with these systems. The engineering community has the opportunity to innovate with liver-on-a-chip devices and collaborate with biomedical researchers to gain a better understanding of liver diseases and develop effective treatments.
Article
Chemistry, Multidisciplinary
Jing Liu, Xiangjun Liu, Mengwen Yi, Yue Sun, Tao Bing, Nan Zhang, Dihua Shangguan
Summary: A photo-activated aptamer-drug conjugate, HG1-9-DNP, was developed, which could release a cytotoxic agent DNNH upon photocleavage, resulting in high photo-induced cytotoxicity.
CHEMICAL COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Jing Lv, Shengnan Li, Xiaoxiao Zhen, Dandan Li, Nan Zhang, Xiangjun Liu, Juanjuan Han, Tao Bing, Dihua Shangguan
Summary: In this study, stable and environmentally sensitive aptamers were optimized from an original cell-binding aptamer. These aptamers selectively captured and released CD49c positive cells, providing a toolbox for studying the heterogeneity of rare cells.
ACS APPLIED BIO MATERIALS
(2022)
