Article
Biophysics
Shuting Li, Longjiao Zhu, Shenghao Lin, Wentao Xu
Summary: Toehold-mediated strand displacement (TMSD) reactions provide a fast, programmable and efficient way for DNA rehybridization. TMSD reactions have been widely used in biochemical sensing and medical diagnosis due to their enzyme-free and isothermal nature. The field faces challenges and has promising prospects.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Analytical
Minghao Hu, Ziyi Chu, Haitao Wang, Wenbo Zhao, Tongbo Wu
Summary: Strand replacement technology faces various and complex applications as a component in the DNA machine and DNA network. By modifying remote toehold-mediated strand displacement, we have enabled it to operate with asymmetric spacer and asymmetric responses to spacer hybridization. Moreover, we have discovered a series of unique modulations, which will expand the application scope of strand displacement technology.
MICROCHEMICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Rebecca P. Chen, Wilfred Chen
Summary: The programmability of nucleic acids allows the design of detection devices with complex behaviors. However, these high-order circuits are often sequence constrained, limiting their adaptability towards biological targets. In this study, a new strategy called indirect associative strand displacement is proposed to overcome the sequence constraints between miRNA inputs and de novo strand displacement circuits.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biophysics
Wenqian Cheng, Zi Lin, Lina Zhao, Ningke Fan, Huijie Bai, Wei Cheng, Min Zhao, Shijia Ding
Summary: An on-off nonenzymatic and ultrasensitive electrochemiluminescence biosensing platform for detecting BCR-ABL fusion gene has been developed based on CeO2/MXene heterojunction and configuration-entropy driven dual-toehold strand displacement reaction. This platform achieves wide concentration variation and low limit of detection, providing new insights for molecular diagnosis of chronic myelogenous leukemia in clinical practice.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Biochemistry & Molecular Biology
Yan Shan Ang, Lin-Yue Lanry Yung
Summary: The research team improved the performance of DNA circuits by dynamically elongating the length of the associative toehold using a hairpin lock design, and established design guidelines to achieve robust elongation without incurring additional leakages. Three hairpin initiators with different combinations of elongated associative toehold were shortlisted from the design framework for further discussion, resulting in improved reaction kinetics, equilibrium signal generation, and limit of detection. Overall, the elongated associative toehold acted as a built-in function to stabilize and favor the forward, desired reaction when triggered.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Engineering, Environmental
Wang Luo, You Wu, Xueping Chen, Li Zhang, Li Wang, Dan Bai, Qian Liu, Ting Wang, Hongyan Yu, Yaxing Xie, Yixin Fu, Zhongzhong Wang, Yujun Yang, Junjie Li, Yongcan Guo, Ke Lv, Guoming Xie
Summary: Combinations of statistically related SNPs, known as haplotypes, can provide richer medical and genetic information than isolated SNPs. However, determining whether SNP loci separated by thousands of bases are located on the same chromosome is challenging and time-consuming. This study developed a mathematical logic-based algorithm, using DNA nanotechnology and thermodynamic mechanisms, to simplify the analysis of long-range haplotypes. The results have the potential to contribute to the development of personalized applications of haplotype analysis.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Physical
Hao Hu, Liquan Liu, Lei Zhang, Wei Zhang, Kejun Dong, Bei Yan, Yaoqin Mu, Mengdi Shi, Longjie Li, Xianjin Xiao
Summary: In this study, we constructed DNA circuits with low leakage by using locked nucleic acids (LNA) to inhibit the breathing effect. Various low-leakage DNA circuits were successfully built, and our strategy did not affect the desired main reactions.
Article
Chemistry, Analytical
Li Li, Zheng Zhou, Xinmin Li, Dandan Li, Min Zhao, Changjin Liu, Haiping Wu, Wei Yang, Shijia Ding, Bo Shen
Summary: A novel 3D walking nanomachine-based biosensor utilizing strand displacement for ultrasensitive detection of ATP was successfully developed, demonstrating a low limit of detection and practical application in human serum samples. This biosensing strategy holds great potential for biochemical studies and clinical diagnosis.
Article
Biophysics
Dan Bai, Xi Zhou, Wang Luo, Hongyan Yu, Shulian Bai, You Wu, Lin Song, Kena Chen, Yaxing Xie, Xueping Chen, Jie Zhao, Yixin Fu, Yujun Yang, Junjie Li, Guoming Xie
Summary: Nucleic acid nanotechnologies based on toehold-mediated strand displacement have shown great potential for detecting single-nucleotide variations (SNVs). In this study, a cooperative hybridization strategy relying on a dual-toehold and bulge-loop (DT & BL) probe, coupled with the strand displacement catalytic (SDC) cycle, was developed to improve the specificity and reaction rate. The feasibility of this platform was demonstrated by successfully identifying cancer-related genes and detecting clinical samples. This study offers a new perspective for constructing highly specific probes based on dynamic DNA nanotechnology, and provides a promising tool for clinical diagnostics.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Analytical
Ni Liao, Mei-Chen Pan, Li Wang, Fan Yang, Ruo Yuan, Ying Zhuo
Summary: A novel swing arm location-controllable DNA walker based on DNA tetrahedral nanostructures was developed for nucleic acid detection, demonstrating enhanced efficiency and potential in diagnostic analysis.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Zhang Zhang, Li Zhang, Youqiang Wang, Juan Yao, Ting Wang, Zhi Weng, Liu Yang, Guoming Xie
Summary: This study introduces an ultrasensitive electrochemical miRNA biosensor based on strand displacement reaction circuits and strand displacement polymerization reaction, demonstrating high sensitivity and discriminatory capability towards let 7a for early cancer screening, providing a new research avenue.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biophysics
Wenchan Deng, Jing Yang Xu, Hanyong Peng, Cheng Zhi Huang, X. Chris Le, Hongquan Zhang
Summary: This study reports a toehold-exchange translator and translator-mediated DNAzyme motor systems that enable sensitive responses to various nucleic acid targets using the same DNAzyme motor without requiring redesign. The translator efficiently converts nucleic acid targets into specific output DNA, activating the DNAzyme motor and enabling autonomous movement. By adjusting the target-binding region of the translator, the same DNAzyme motor system can respond to multiple nucleic acid targets. The study also demonstrates the construction and operation of four logic gates using the translator and DNAzyme motor, enhancing the biosensing applications of DNA motors.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Biophysics
Xiaolei Song, Qin Ding, Yuepu Pu, Juan Zhang, Rongli Sun, Lihong Yin, Wei Wei, Songqin Liu
Summary: A new non-label and enzyme-free fluorescence biosensor for highly specific detection of OTA was developed using TMSD and G-dimer/ThT. The method successfully analyzed OTA in real food samples, offering a new way for OTA and other toxin analysis detection.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Multidisciplinary Sciences
Chisato Terada, Kaho Oh, Ryutaro Tsubaki, Bun Chan, Nozomi Aibara, Kaname Ohyama, Masa-Aki Shibata, Takehiko Wada, Mariko Harada-Shiba, Asako Yamayoshi, Tsuyoshi Yamamoto
Summary: In this study, a toehold-bearing ASO architecture is developed to mitigate a broad spectrum of off-target interactions, significantly enhancing the safety profile of ASO drugs.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Yeru Wang, Yu Wang, Su Liu, Wenyu Sun, Manru Zhang, Long Jiang, Minghan Li, Jinghua Yu, Jiadong Huang
Summary: A smart tripedal DNA walker is designed in this research, which can move freely on the electrode with improved walking efficiency, eliminating the drawbacks of high cost and instability, showing potential in OTA detection applications.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Analytical
Jing Zhang, Dongzhi Wu, QiuXiang Chen, Mei Chen, Yaokun Xia, Shuxian Cai, Xi Zhang, Fang Wu, Jinghua Chen
Article
Biophysics
Xianghui Li, Longjie Gan, Qishui Ou, Xi Zhang, Shuxian Cai, Dongzhi Wu, Mei Chen, Yaokun Xia, Jinghua Chen, Bin Yang
BIOSENSORS & BIOELECTRONICS
(2015)
Article
Chemistry, Analytical
Shuxian Cai, Guangwen Li, Xi Zhang, Yaokun Xia, Mei Chen, Dongzhi Wu, Qiuxiang Chen, Jing Zhang, Jinghua Chen
Article
Chemistry, Multidisciplinary
Jianming Lan, Fadi Wen, Fangmeng Fu, Xi Zhang, Shuxian Cai, Zhijing Liu, Dongzhi Wu, Chunyan Li, JingHua Chen, Chuan Wang
Editorial Material
Chemistry, Multidisciplinary
Joseph T. Buchman, Miranda J. Gallagher, Chi-Ta Yang, Xi Zhang, Miriam O. P. Krause, Rigoberto Hernandez, Galya Orr
ENVIRONMENTAL SCIENCE-NANO
(2016)
Article
Chemistry, Multidisciplinary
Joseph T. Buchman, Ali Rahnamoun, Kaitlin M. Landy, Xi Zhang, Ariane M. Vartanian, Lisa M. Jacob, Catherine J. Murphy, Rigoberto Hernandez, Christy L. Haynes
ENVIRONMENTAL SCIENCE-NANO
(2018)
Article
Biophysics
Jing Hua Chen, Xi Zhang, Shuxian Cai, Dongzhi Wu, Jia Lin, Chunyan Li, Jing Zhang
BIOSENSORS & BIOELECTRONICS
(2014)
Article
Chemistry, Multidisciplinary
Eric S. Melby, Caley Allen, Isabel U. Foreman-Ortiz, Emily R. Caudill, Thomas R. Kuech, Ariane M. Vartanian, Xi Zhang, Catherine J. Murphy, Rigoberto Hernandez, Joel A. Pedersen
Article
Chemistry, Analytical
Xi Zhang, Arun Kumar Pandiakumar, Robert J. Hamers, Catherine J. Murphy
ANALYTICAL CHEMISTRY
(2018)
Article
Chemistry, Multidisciplinary
Emily J. Tollefson, Caley R. Allen, Gene Chong, Xi Zhang, Nikita D. Rozanov, Anthony Bautista, Jennifer J. Cerda, Joel A. Pedersen, Catherine J. Murphy, Erin E. Carlson, Rigoberto Hernandez
Article
Chemistry, Multidisciplinary
Xi Zhang, Priscila Falagan-Lotsch, Catherine J. Murphy
Summary: Engineered colloidal nanoparticles have great potential in biomedical applications, with the ability to indirectly affect cell behavior by sequestering molecules from the biological environment. Experimental results demonstrate that gold nanoparticles with specific surface chemistries can significantly reduce chemotaxis of THP-1 cells.
Article
Chemistry, Analytical
Guanyu Chen, Wenqian Chen, Lilan Xu, Huixuan Jin, Weiming Sun, Jianming Lan, Fang Wu, Xi Zhang, Jing Zhang, Jinghua Chen
Summary: This research proposes a self-assembled electrode that combines different materials to address the challenges of electrochemical biosensors in practical applications. By using hexanethiol for forming a self-assembled monolayer, cholesteryl-modified DNA for increasing assembly efficiency and uniformity, and poly-adenine for enhancing anti-fouling ability, a dual-signal amplification electrochemical biosensor is developed for the detection of exosomal microRNAs, showing great sensitivity and potential utility in cancer diagnosis.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Jingrong Liu, Chunxiao Yu, Luodan Han, Yiping Shen, Yao Fang, Yaokun Xia, Xu Yao, Fang Wu, Chunyan Li, Jinghua Chen, Xi Zhang, Jianming Lan
Summary: A wash-free biological aptasensor based on UCNPs and TAMRA was developed for high sensitive detection of TSH. The sensor achieved detection by changing the distance between UCNPs and TAMRA, and effectively eliminated background interference. With its high sensitivity and operational convenience, it is a promising method for clinical TSH determination.
Article
Nanoscience & Nanotechnology
Tingting Chen, Bingxiang Ma, Shi Lu, Lupeng Zeng, Huaying Wang, Wanhua Shi, Linying Zhou, Yaokun Xia, Xi Zhang, Jing Zhang, Jinghua Chen
Summary: Cucumber-derived nanovesicles (CDNVs) obtained by simple juicing and ultracentrifugation exhibit strong anticancer effects both in vitro and in vivo. CDNVs inhibit the proliferation of non-small cell lung cancer cells, reduce tumor growth in mice, and show no obvious toxicity to mouse visceral organs. CDNVs exert stronger anticancer effects compared to cucurbitacin B.
INTERNATIONAL JOURNAL OF NANOMEDICINE
(2022)
Article
Chemistry, Analytical
Luodan Han, Liu Yan, Chunxiao Yu, Yingxin Liu, Fang Wu, Xi Zhang, Xu Yao, Chunyan Li, Jinghua Chen, Xiaosong Chen, Jianming Lan
Summary: By simple refitting, a weak light photodetector can be used for highly sensitive detection of upconversion luminescence (UCL) signal of NaYF4:Yb/Er upconversion nanoparticles (UCNPs). A label-free biosensor is designed for selective detection of glutathione (GSH) based on the UCL quenching mechanism of the inner-filter effect (IFE) between UCNPs and MnO2 nanosheet. The photodetector shows excellent stability and sensitivity, with a linear range of 0.1-100 μM and a detection limit of 41 nM.
MICROCHEMICAL JOURNAL
(2023)
