Article
Chemistry, Multidisciplinary
Yuwei Hu, Yujie Ke, Itamar Willner
Summary: A cascaded DNA hydrogel governed by pH-configurable A-motif, i-motif, and T·A-T triplex configurations is presented. Different pH conditions dictate the formation and stability of the hydrogel through the protonation and deprotonation of adenine and cytosine residues. This study advances the development of smart hydrogels capable of adapting to various environmental conditions by introducing multiple pH-responsiveness.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
Yuwei Hu, Jackie Y. Ying
Summary: Smart DNA hydrogels containing dynamic reconfigurable DNA crosslinking units exhibit sol-gel transition, shape memory, self-healing, sensing, cargo encapsulation, and delivery. They are designed to respond to external stimuli such as light, pH, ions, fuel strands, thermal triggers, chemical, and biocatalytic reactions for various applications in material science, chemistry, and biomedicine. This review focuses on the recent advances in pH-sensitive nucleic acid structures, particularly A-motif, i-motif, and triplex, for pH-responsive DNA hydrogels. The review discusses the structural details of pH-triggered A-motif, i-motif, and triplex configurations as the foundation for constructing pH-responsive DNA hydrogels, as well as the physicochemical properties and applications of these hydrogels in shape modulation, self-healing, drug release, sensing, therapy, and soft matter.
Article
Biophysics
Anton Turaev, Ekaterina A. Isaakova, Vjacheslav V. Severov, Alexandra N. Bogomazova, Timofei S. Zatsepin, Makar Sardushkin, Andrey Aralov, Maria A. Lagarkova, Galina E. Pozmogova, Anna M. Varizhuk
Summary: The design of robust sensors for measuring intracellular pH based on native DNA i-motifs offers a sensitive and fast-response approach without the need for additional modules. This 'genome-inspired' design can be used to monitor proton dynamics in the nucleus, suggesting it is a productive approach for the development of biocompatible molecular tools.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Chemistry, Multidisciplinary
Mingpan Cheng, Dehui Qiu, Liezel Tamon, Eva Istvankova, Pavlina Viskova, Samir Amrane, Aurore Guedin, Jielin Chen, Laurent Lacroix, Huangxian Ju, Lukas Trantirek, Aleksandr B. Sahakyan, Jun Zhou, Jean-Louis Mergny
Summary: Recent studies have shown that i-DNA, a four-stranded cytosine-rich DNA known as the i-motif, is formed in vivo. This study tested 271 different sequences and found that i-DNA stability is nearly independent on total spacer length, with the central spacer playing a special role in stability. The study also revealed that stability depends on the length of the C-tracts at both acidic and neutral pHs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Spectroscopy
Tong Yang, Shuzhen Peng, Ruidi Zeng, Qiuda Xu, Xiong Zheng, Dandan Wang, Xiaoshun Zhou, Yong Shao
Summary: This study developed a visible light-driven DNAzyme based on human telomeric i-motifs, using hypericin as the cofactor and dissolved oxygen as the oxidant source. The DNAzyme has broad applications and its catalytic performance can be improved using a long-lived mediator.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Biochemistry & Molecular Biology
Francesca Greco, Maria Marzano, Andrea Patrizia Falanga, Monica Terracciano, Gennaro Piccialli, Giovanni Nicola Roviello, Stefano D'Errico, Nicola Borbone, Giorgia Oliviero
Summary: This study reports the design of structurally modified CROs, called DEL-CROs, which can form more stable i-motif structures compared to unmodified CROs. This opens up possibilities for developing pH-switchable nanocarriers and aptamers based on DEL-CROs.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Analytical
Huanhuan Xing, Yazhen Zhu, Dangdang Xu, Ruili Wu, Xiaojing Xing, Lin Song Li
Summary: This study aimed to construct a novel DNA triplex molecular switch (DTMS-DT) with sensitive response to extracellular pH using a DNA tetrahedron as the anchoring unit and DNA triplex as the response unit. The results showed that DTMS-DT had desirable pH sensitivity, reversibility, anti-interference ability, and biocompatibility. Confocal laser scanning microscopy suggested that DTMS-DT could be stably anchored on the cell membrane and used to monitor the change in extracellular pH. Compared with reported probes, the designed DNA tetrahedron-mediated triplex molecular switch exhibited higher stability and reliability for extracellular pH monitoring.
ANALYTICA CHIMICA ACTA
(2023)
Article
Chemistry, Multidisciplinary
Shiliang He, Mengmeng Liu, Fangfei Yin, Jiangbo Liu, Zhilei Ge, Fan Li, Min Li, Jiye Shi, Lihua Wang, Xiuhai Mao, Xiaolei Zuo, Qian Li
Summary: The response sensitivity of a molecular sensor depends on the folding cooperativity of its responsive module. This can be enhanced through preorganization, as demonstrated with an H+-responsive dimeric DNA i-motif, to create robust intracellular pH sensors with high response sensitivity.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Bin Wang, Eric Chatterton
Summary: This study investigates the feasibility of using capillary electrophoresis as an alternative method for i-motif related research, with results showing that capillary electrophoresis can identify and differentiate different states of DNA and RNA i-motifs through changes in peak shape and migration time.
Article
Biotechnology & Applied Microbiology
Baoyin Yuan, Yanan Xi, Cuihua Qi, Mingzhu Zhao, Xiaoyan Zhu, Jinlu Tang
Summary: A smart dual-targeted DNA nanocapsule was designed with a sequentially triggered strategy based on double targeting elements, providing precise and selective delivery of chemotherapeutics to tumor cells while inhibiting migration and invasion.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Analytical
Neeraj Bangruwa, Prashant K. Bhartiya, Debabrata Mishra
Summary: In this study, a spin-based label-free DNA hybridization sensor was developed using spin-polarized electrons as a detection tool. The sensor takes advantage of chiral-induced spin selectivity to directly probe the hybridization of DNA. A self-assembled monolayer of DNA was prepared on Au-coated Ni devices, and the hybridization phenomena were investigated using differential pulse voltammetry. The accuracy of the sensor was tested using complementary techniques, and it was successfully applied for detecting the Dengue virus with a limit of detection of 0.12 picomolar (pM). This approach opens up new possibilities for future spin-based point-of-care devices.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Nanoscience & Nanotechnology
Huihui Yang, Jun Chen, Yuling Liang, Yanfei Zhang, Wen Yin, Yuzhi Xu, Si-Yang Liu, Zong Dai, Xiaoyong Zou
Summary: This study presents a novel MOFC-i strategy for sensitive and dynamic imaging of cell surface pH using optimized pH probes and microporous MOF shell. The method can distinguish different metabolic behaviors of cancer cells and normal cells, and assess drug effects on cell surface pH or metabolism.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Organic
Puja Saha, Deepanjan Panda, Raj Paul, Jyotirmayee Dash
Summary: The gold nanoparticle-based DNA nanosensor presented in this study can detect the formation of an i-motif from a random coil structure by small molecules at physiological pH, showing a distance dependent fluorescence turn-off response in the presence of a ligand.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Spectroscopy
Jan Palacky, Petra Skolakova, Daniel Renciuk, Peter Mojzes, Barbara Rossi, Fatima Matroodi, Michaela Vorlickova
Summary: In this study, off-resonant and UV-resonant Raman spectroscopy were used to investigate the iM formation of the (C9T3)3C9 sequence at neutral pH. The results showed that different iM species with varying thermal stability and kinetic properties are formed at different temperatures. The sequence exists as a mixture of disordered and ordered structures.
JOURNAL OF RAMAN SPECTROSCOPY
(2023)
Article
Chemistry, Multidisciplinary
Michele Ghezzo, Marko Trajkovski, Janez Plavec, Claudia Sissi
Summary: A new pipeline was developed for the systematic screening of model sequences that can form i-Motifs. It was found that two and three nucleotides are required to connect the strands through the minor and major grooves of the iM, respectively. Additionally, the distribution of cytosines showed an asymmetric behavior in forming stable intra-molecular iMs. This study provides important knowledge for the prediction and design of biologically functional iMs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Wen Shou, Yueliang Wang, Yuanyuan Yao, Lifen Chen, Binyong Lin, Zhenyu Lin, Longhua Guo
Summary: Monitoring temperature change is crucial for ensuring the safety and efficacy of temperature-sensitive products. Traditional digital thermometers have limitations in cost, recording capabilities, and vulnerability to tampering. Therefore, the development of multicolor plasmonic hydrogels as a full-history time-temperature indicator (FHTTI) provides a valuable solution for accurately and comprehensively indicating the time and temperature history of products.
ANALYTICA CHIMICA ACTA
(2023)
Article
Chemistry, Analytical
Qin Luo, Mengjian Tian, Fang Luo, Min Zhao, Cuiying Lin, Bin Qiu, Jian Wang, Zhenyu Lin
Summary: This study established an innovative multicolor sensor for trypsin detection, based on the regulation of the peroxidase activity of BSA-Au NCs and efficient etching of Au NBPs. The designed sensor has a linear relationship with the logarithm of trypsin concentration, with a detection limit of 0.045 μg/mL. It has been successfully applied to analyze trypsin concentration in human serum samples from healthy individuals and pancreatitis patients.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Cuiying Lin, Qingqing Huang, Mengjian Tian, Fang Luo, Jian Wang, Bin Qiu, Shuofei Yang, Zhenyu Lin
Summary: An electrochemiluminescence (ECL) biosensor with dual signal enhancement was developed to detect DNA adenine methylation methyltransferase (Dam MTase). The biosensor utilized a restriction endonuclease to cleave DNA and activate CRISPR/Cas12a trans-cleavage activity, resulting in enhanced ECL signal. The biosensor exhibited a good linear relationship with Dam MTase concentration and was successfully applied for detection in serum samples.
Article
Agriculture, Multidisciplinary
Tong Li, Ruiguo Wang, Ruijie Yin, Hongyan Xu, Xiaoxu Han, Qiuling Du, Jie Cheng, Zhenyu Lin, Peilong Wang
Summary: A novel Zr(IV)-based metal-organic framework (MOF), named BUT-16, was synthesized and utilized for the extraction and enrichment of bisphenol compounds (BPs) in milk samples. The method showed a detection limit as low as 0.05 ng/mL and was successfully applied to the detection of BPs in real milk samples, yielding results consistent with previous methods.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Liang Wang, Ying Cheng, Cuiqin Wu, Fang Luo, Zhenyu Lin, Ravi Naidu
Summary: The study used SPME to sample soil gas and GC/MS to detect petroleum hydrocarbon volatile organic compounds (pH-VOCs) in underground pipeline leaks. By optimizing the extraction method and sample conditioning, the analytical efficiency and accuracy were improved, resulting in reliable research data with minimized environmental impacts.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Analytical
Liangzhen Xu, Shuang Hou, Xiaocui Huang, Mengyuan Wang, Cheng Li, Nuo Dong, Zhenyu Lin
Summary: A homogeneous electrochemiluminescence (ECL) biosensor based on catalyze hairpin assembly (CHA) and hybridization chain reaction (HCR) and magnetic assisted enrichment has been developed for miR-155 detection in dry eye diseases caused by Sjogren's syndrome. The biosensor offers a simple and sensitive detection method and has been successfully applied in clinical samples.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Weiquan Wang, Yunpeng Xu, Jie Hou, Zhixin Li, Fang Luo, De He, Zhenyu Lin
Summary: A HAase-responsive hydrogel system was designed to semi-quantitatively determine HAase by utilizing the relationship between HAase and spilled H2O2. Additionally, Au NRs were etched by H2O2, and the color change of the solution was used as a semi-quantitative method for HAase determination. The proposed method has been successfully applied to monitor HAase in serum of pancreatic cancer patients.
Review
Chemistry, Multidisciplinary
Liang Wang, Ying Cheng, Saianand Gopalan, Fang Luo, Khairunnisa Amreen, Ritesh Kumar Singh, Sanket Goel, Zhenyu Lin, Ravi Naidu
Summary: Currently, various advanced methods are being used in gas sensing and monitoring, including detecting hazardous gas leaks and monitoring ambient air. Commonly used technologies include photoionization detectors, electrochemical sensors, and optical infrared sensors. However, these sensors, which are nonselective or semiselective, can be affected by unwanted analytes. To address this issue, gas separation and discrimination technologies such as gas permeable membranes, metal-organic frameworks, microfluidics, and IR bandpass filters have been developed. Although these technologies have not been extensively utilized in the field for vapor intrusion monitoring, they show promise for further development and application. This review provides an overview and summary of the existing gas separation and discrimination technologies for popular gas sensors used in environmental applications.
Article
Chemistry, Analytical
Qin Luo, Yu Chen, Lifen Chen, Zhonghui Chen, Fang Luo, Jian Wang, Cuiying Lin, Bin Qiu, Longhua Guo, Zhenyu Lin
Summary: A multicolor sensor based on the inhibition of peroxidase activity and color change caused by etching of gold nanobipyramids was constructed for Hg2+ detection. The sensor can achieve semi-quantitative detection using the multicolor changes of the gold nanobipyramids and quantitative sensing by measuring the UV-vis peak shift. The linear response range is 1.0 nM-10 μM, and the detection limit is 0.28 nM.
MICROCHEMICAL JOURNAL
(2023)
Article
Chemistry, Analytical
Yunpeng Xu, Jiahui Chen, Xiaolu Sui, Yanzi Zhang, Aisha Zhang, Zhenyu Lin, Xinguang Liu, Jihong Chen
Summary: The study developed an ultra-sensitive biosensor for microRNA-21 (miRNA-21) by combining the high selectivity and trans-cleavage activity of CRISPR/Cas13a, the high amplification efficiency of HCR, and the high sensitivity of ECL detection. The biosensor recognized target RNA using CRISPR/Cas13a and performed trans-cleavage activity. A signal amplification was achieved by generating long dsDNAs through HCR, and ECL intensity was measured using Ru(phen)32+ as an indicator. The system showed good linear correlation and a limit of detection (LOD) of 0.53 fM for miRNA-21, and was successfully applied to detect miRNA-21 in the urine of acute kidney injury (AKI) patients.
Article
Chemistry, Analytical
Yifan Jiang, Huilan Zhang, Meizhu Xu, Fang Luo, Cuiying Lin, Bin Qiu, Zhenyu Lin, Zhou Jiang, Jian Wang
Summary: A novel photoelectrochemical (PEC) sensor was constructed for highly sensitive detection of reduced glutathione (GSH) using the catalytic properties of phosphotungstic acid (PTA). PTA acts as an electron acceptor, increasing the photogenerated current of Cu2O by inhibiting electron-hole complexation. It also facilitates the regeneration of GSH by reducing oxidized glutathione (GSSG) through proton transfer. Additionally, PTA pre-oxidizes interfering substances, improving the selectivity of the method. The PEC sensor showed a linear response to GSH in the range of 0.050-100 nmol L-1, with a low detection limit of 0.017 nmol L-1 (S/N = 3) for GSH content detection in cell lysate samples.
Article
Chemistry, Analytical
Qin Luo, Mengjian Tian, Fang Luo, Min Zhao, Cuiying Lin, Bin Qiu, Jian Wang, Zhenyu Lin
Summary: In this study, a novel multicolor sensor for trypsin detection has been developed based on the regulation of peroxidase activity of BSA-Au NCs. By hydrolyzing BSA ligands on the surface of BSA-Au NCs, trypsin exposes more catalytic active sites of BSA-Au NCs, enhancing their peroxidase activity, resulting in the generation of more TMB+. Under acidic conditions, TMB+ effectively etches Au NBPs, changing their aspect ratio and causing a blue shift in the UV-vis spectra.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Weixin Li, Xinyang Wang, Jiaji Huang, Min Zhao, Jiao Yang, Fang Luo, Bin Qiu, Jian Wang, Zhenyu Lin
Summary: In this work, three-dimensional ZnO nanostructures were used as the support for gold nanoparticles and graphite carbon nitride to form a Z-scheme heterostructure photoelectrode. The photoelectrode exhibited fast carrier transport and abundant reaction sites, and the gold nanoparticles acted as mediators to enhance electron transfer. The developed photoelectrochemical biosensor based on the Z-scheme heterostructure showed good sensitivity and selectivity for the detection of reduced glutathione.
SENSORS & DIAGNOSTICS
(2023)
Article
Chemistry, Analytical
Cheng Chen, Jing Li, Fang Luo, Zhenyu Lin, Jian Wang, Tao Zhang, Aiwen Huang, Bin Qiu
Summary: In this study, a Eu MOF was used to encapsulate FeNCDs, resulting in increased dispersibility and enzymatic catalytic efficiency. The FeNCDs@Eu MOF-based sensor exhibited a nearly 6-fold increase in response to tetracycline, with a low detection limit of 11.63 nM.
Article
Chemistry, Analytical
Jing Li, Cheng Chen, Fang Luo, Cuiying Lin, Zhenyu Lin, Jian Wang, Bin Qiu
Summary: A dual-signal mode ratiometric photoelectrochemical (PEC) sensor based on a Au/GaN photoanode is proposed for rapid and sensitive detection of miRNA-210, crucial for improving the reliability of clinical diagnosis of breast cancer. The sensor utilizes a specially designed DNA probe and a G-rich DNA sequence to enable label-free and sensitive detection of miRNA-210. The potential of this PEC sensor for miRNA-210 detection and other disease markers is demonstrated.
ANALYTICAL CHEMISTRY
(2023)
