Article
Chemistry, Multidisciplinary
Thomas Mayer, Lukas Oesinghaus, Friedrich C. Simmel
Summary: We investigated the impact of random DNA sequences on TMSD circuits and found that only a small subpopulation of strongly interacting strands determined the kinetics. We also compared three techniques to speed up TMSD reactions and found that only the last one can be used without sequence constraints.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
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
Jian Zhu, Zhu Su, Bin Yang, Li Peng, Huimin Hao, Shuyan Lou
Summary: In this study, a new signal translator was developed to assay progesterone using a DNA transient molecular event and an exonuclease-mediated strategy. The aptamer probe showed good selectivity for progesterone and robust signal response in real samples, making it suitable for environmental or clinical analysis.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biophysics
Yanmin Gao, Hongyan Qiao, Victor Pan, Zhaoguan Wang, Jiaojiao Li, Yanan Wei, Yonggang Ke, Hao Qi
Summary: In this study, a new approach for accurate genotyping of highly fragmented DNA was presented, with toehold-assisted padlock probe systems designed for 14 different single-nucleotide variants. By combining toehold-mediated strand displacement technology, precise genotyping of low concentration variant alleles in liquid biopsy samples was achieved, offering a new commercial approach for high-resolution genetic variation analysis.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Chemistry, Multidisciplinary
Erica Del Grosso, Patrick Irmisch, Serena Gentile, Leonard J. Prins, Ralf Seidel, Francesco Ricci
Summary: This study presents a general approach to achieve dissipative control over toehold-mediated strand-displacement, a widely used reaction in DNA nanotechnology. By re-engineering the classic reaction, the high-energy invader strand is converted into a low-energy waste product, allowing the system to spontaneously return to its original state over time. This method enables unique temporal activation of DNA systems and is reversible and highly controllable.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Guan Alex Wang, Xinghong Wu, Fangfang Chen, Chenlan Shen, Qianfan Yang, Feng Li
Summary: This article presents a method for designing aptamer switches with improved thermal robustness and programmability, using toehold-exchange as a general framework. Experimental results demonstrate that this method not only enhances the thermal stability of aptamer switches, but also improves their analytical performances and programmability.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Roser Montagud-Martinez, Maria Heras-Hernandez, Lucas Goiriz, Jose-Antonio Daros, Guillermo Rodrigo
Summary: DNA nanotechnology and DNA computing have seen significant advancements over the past decade, resulting in a variety of functional stable structures and dynamic circuits. A new study utilized CRISPR-Cas systems to engineer logic circuits based on isothermal strand displacement, demonstrating good interoperability and expanding the repertoire of substrates and reactions for DNA computing.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Sai Sumanjali Yarra, Ganapathy Ashok, Utpal Mohan
Summary: Toehold switches are newly designed riboregulators with two RNA components and linear-linear RNA interactions, providing regulation of gene expression. They are highly versatile, orthogonal, programmable, and find applications in various fields of synthetic biology.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Su-Rung Yang, Ying-Yu Yeh, Yi-Cheun Yeh
Summary: The study explores the use of ultrasound-initiated thiol-norbornene reaction for fabricating hydrogels and investigates how ultrasound conditions determine the properties of the hydrogels.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Jinbo Zhu, Filip Boskovic, Bao-Nguyen T. Nguyen, Jonathan R. Nitschke, Ulrich F. Keyser
Summary: Introducing an external stimulus (Fe4L4)-L-II tetrahedral cage enables modulation of SDR kinetics. The binding of the cage on the toehold end slows down SDR, while stabilizing intermediates containing two overhangs accelerates the reaction.
Article
Chemistry, Analytical
Xiaotong Shen, Qingwen Ouyang, Hongwei Tan, Jin Ouyang, Na Na
Summary: Researchers designed stable single-stranded DNA (ssDNA) nanorobots by examining the dynamic folding of ssDNA in self-assemblies via molecular dynamics simulations. Two ssDNA strands were successfully assembled into nanorobots using two functional siRNAs, enabling multiple applications. The nanorobots were demonstrated to be stable, flexible, highly utilized, and low in folding errors. This study provides a computational pathway for constructing flexible and multifunctional ssDNA frameworks, expanding the biological application of nucleic acid nanostructures.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
You Wu, Wang Luo, Zhi Weng, Yongcan Guo, Hongyan Yu, Rong Zhao, Li Zhang, Jie Zhao, Dan Bai, Xi Zhou, Lin Song, Kena Chen, Junjie Li, Yujun Yang, Guoming Xie
Summary: CRISPR technology has achieved great breakthroughs and is becoming the most promising molecular tool. This research proposes a novel CRISPR/Cas12a activation mode to improve its performance and broaden its application boundaries, which eliminates the need for protospacer adjacent motif and accurately activates Cas12a through toehold-mediated strand displacement and branch migration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Shaohua Xu, Yueliang Wang, Yuanyuan Yao, Lifen Chen, Jiahui Xu, Bin Qiu, Longhua Guo
Summary: This study proposed a highly sensitive strategy for miRNA-21 detection using programmable toehold-mediated strand displacement (TMSD) and dark-field microscopy imaging. The method achieved highly specific recognition and amplification of miRNA-21 through the hybridization of assist strands and substrate strand. By modifying glucose oxidase (Gox) on the assist strands, the size and scattering intensity of Au@Ag NCs were reduced, allowing for the quantitative detection of miRNA-21.
Article
Chemistry, Analytical
Yinping Deng, Jun Du, Donghua Chen, Guo-Jiang Mao, Bin Yang, Yin Zhang, Zhu Su, Hanfen Cai
Summary: A novel junction toehold with low signal leakage is reported in this study, which cooperatively and sequentially activates DNA strand displacement process by two inputs with independent oligonucleotide sequences, allowing kinetics to be flexibly tuned independently by multi-parameters.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
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)
Review
Chemistry, Multidisciplinary
Yongxi Zhao, Xiaolei Zuo, Qian Li, Feng Chen, Yan-Ru Chen, Jinqi Deng, Da Han, Changlong Hao, Fujian Huang, Yanyi Huang, Guoliang Ke, Hua Kuang, Fan Li, Jiang Li, Min Li, Na Li, Zhenyu Lin, Dingbin Liu, Juewen Liu, Libing Liu, Xiaoguo Liu, Chunhua Lu, Fang Luo, Xiuhai Mao, Jiashu Sun, Bo Tang, Fei Wang, Jianbin Wang, Lihua Wang, Shu Wang, Lingling Wu, Zai-Sheng Wu, Fan Xia, Chuanlai Xu, Yang Yang, Bi-Feng Yuan, Quan Yuan, Chao Zhang, Zhi Zhu, Chaoyong Yang, Xiao-Bing Zhang, Huanghao Yang, Weihong Tan, Chunhai Fan
Summary: Nucleic acids are natural biopolymers that play central roles in storing, encoding, transmitting and expressing genetic information. The field of nucleic acids analysis has rapidly advanced with technological breakthroughs, leading to the development of new analysis methods. However, there are also challenges and further research needed in this area.
SCIENCE CHINA-CHEMISTRY
(2021)
Article
Engineering, Biomedical
Richard Johnson, Michael Rafuse, Prakash Parthiban Selvakumar, Wei Tan
Summary: This study evaluated the impacts of allogeneic bone marrow-derived stromal cells and recipient age on the long-term remodeling of vascular grafts. The results showed significant effects of these factors on graft outcomes. Additionally, compared to acellular grafts, cellular grafts showed efficient recruitment of vascular cells to form more organized structures.
ACTA BIOMATERIALIA
(2021)
Article
Chemistry, Physical
Yaxin Yu, Wei Tan, Dongqi An, Xiuwen Wang, Annai Liu, Weixin Zou, Changjin Tang, Chengyan Ge, Qing Tong, Jingfang Sun, Lin Dong
Summary: Research has shown that SO2 poisoning of NH3-SCR catalysts at low temperature remains a challenge. The formation of sulfate species inhibits the adsorption of NOx, while the formation of ferric sulfate enhances surface acidity, leading to an increase in catalytic activity.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2021)
Article
Engineering, Environmental
Wei Tan, Annai Liu, Shaohua Xie, Yong Yan, Thomas E. Shaw, Yu Pu, Kai Guo, Lulu Li, Shuohan Yu, Fei Gao, Fudong Liu, Lin Dong
Summary: Investigating catalytic reaction mechanisms can guide catalyst design, as demonstrated by the innovative CeO2-SiO2 mixed oxide catalyst (CeSi2) with excellent SO2/H2O resistance in harsh working conditions. The strong Ce-O-Si interaction and abundant surface hydroxyl groups on CeSi2 provide active acid sites and inhibit SO2 adsorption, enhancing the NH3-SCR performance through an enhanced Eley-Rideal mechanism. This work offers a strategy to develop an environmentally friendly NH3-SCR catalyst with superior SO2 resistance.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Fujian Huang, Mengxi Chen, Zhixin Zhou, Ruilin Duan, Fan Xia, Itamar Willner
Summary: Understanding the effects of surface topographies and modulated stiffness and anisotropic stresses of hydrogels on cell growth is a biophysical challenge. Researchers have introduced photolithographic patterning or two-photon laser scanning confocal microscopy patterning of nucleic acid-based polyacrylamide hydrogel films to control cell behavior. They demonstrate the patterning of physical and biochemical properties to tune local cell responses.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Applied
Wei Tan, Jin Wang, Yandi Cai, Lulu Li, Shaohua Xie, Fei Gao, Fudong Liu, Lin Dong
Summary: This study proposes a new strategy of Mo doping to improve the low-temperature SCR activity of CeSi2. A Mo-Ce-Si mixed-oxide catalyst was prepared by a simple co-precipitation method. Mo doping significantly enhances the NH3-SCR activity of CeSi2 and exhibits superior N2 selectivity and resistance to SO2/H2O poisoning.
Article
Chemistry, Multidisciplinary
Wang Song, Jiawei Ji, Kai Guo, Xin Wang, Xiaoqian Wei, Yandi Cai, Wei Tan, Lulu Li, Jingfang Sun, Changjin Tang, Lin Dong
Summary: CeO2/TiO2 catalysts prepared by solid-phase impregnation showed better catalytic activity in low-temperature selective catalytic reduction of NOx with NH3. Surface changes of TiO2 were found to have a significant impact on the improved activity.
CHINESE CHEMICAL LETTERS
(2022)
Article
Chemistry, Applied
Lulu Li, Jiawei Ji, Wei Tan, Wang Song, Xin Wang, Xiaoqian Wei, Kai Guo, Wanyu Zhang, Changjin Tang, Lin Dong
Summary: In this work, a supported catalyst consisting of FeOx and MnOx co-supported on aluminum-modified CeO2 was synthesized and applied in the low-temperature NH3-selective catalytic reduction (NH3-SCR) of NO. The study revealed that the SCR activity of the catalyst was significantly influenced by the amount of added aluminum and the appropriate Ce/Al molar ratio. The Fe-Mn/Ce1Al2 catalyst exhibited over 90% NO conversion at a temperature range of 75-250 degrees Celsius and displayed better resistance to SO2 compared to FeeMn/CeO2.
JOURNAL OF RARE EARTHS
(2022)
Article
Chemistry, Physical
Shaohua Xie, Wei Tan, Yuejin Li, Lu Ma, Steven N. Ehrlich, Jiguang Deng, Peng Xu, Fei Gao, Lin Dong, Fudong Liu
Summary: In this study, an efficient NbCuCe oxide catalyst for reducing NOx emissions in cold-start diesel engines is reported. The catalyst exhibits higher DeNO(x) activity below 200 degrees C compared to the Cu-CHA zeolite catalyst, along with superior sulfur resistance, faster response, and lower NH3 slip. Atomically dispersed Cu species facilitate strong interaction between Cu and the Nb/Ce base catalyst, leading to improved low-temperature redox properties and NH3 adsorption/activation. The developed NbCuCe catalyst shows promising potential for efficient DeNO(x) in cold-start diesel engines and can be combined with Cu-CHA for a broader temperature range of operation.
Article
Chemistry, Multidisciplinary
Shaohua Xie, Liping Liu, Yu Lu, Chunying Wang, Sufeng Cao, Weijian Diao, Jiguang Deng, Wei Tan, Lu Ma, Steven N. Ehrlich, Yaobin Li, Yan Zhang, Kailong Ye, Hongliang Xin, Maria Flytzani-Stephanopoulos, Fudong Liu
Summary: The local coordination structure of metal sites plays a crucial role in the performance of supported metal catalysts. This study successfully fabricated Pt atomic single-layer structures with precisely controlled local coordination environment, which exhibited higher turnover frequency and improved catalytic activity in CO oxidation. This work provides new insights for achieving 100% atomic utilization efficiency and optimal intrinsic catalytic activity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Wei Tan, Shaohua Xie, Xin Wang, Juntian Xu, Yong Yan, Kaili Ma, Yandi Cai, Kailong Ye, Fei Gao, Lin Dong, Fudong Liu
Summary: In this study, an efficient CuO catalyst supported on a CeO2-Al2O3 support (CA-T) prepared by two-step incipient wetness impregnation (T-IWI) method was successfully developed. The Cu/CA-T catalyst exhibited better catalytic performance in CO oxidation and NO reduction by CO (NO + CO reaction) as well as higher thermal stability compared to the CuO catalyst loaded on conventional CeO2-Al2O3 support (Cu/CA). The microstructure of CuO-CeO2-Al2O3 catalysts, especially the state of Cu species, was systematically investigated using various characterization techniques. The mechanisms of CO oxidation and NO + CO reactions on Cu/CA and Cu/CA-T catalysts were collaboratively revealed.
Article
Chemistry, Multidisciplinary
Qinglong Liu, Peng Yang, Wei Tan, Haowei Yu, Jiawei Ji, Cong Wu, Yandi Cai, Shaohua Xie, Fudong Liu, Song Hong, Kaili Ma, Fei Gao, Lin Dong
Summary: The size effect on nanoparticles plays a crucial role in catalysis performance. Tuning the oxygen vacancies on a metal-oxide support can help reduce the size of Pt particles, thus improving the catalysis performance of the supported catalyst. In this study, Ce-Sn solid solutions (CSO) with abundant oxygen vacancies were synthesized. After CO reduction, the catalytic CO oxidation performance of Pt/CSO was significantly better than that of Pt/CeO2. This improvement was attributed to the creation of smaller Pt clusters on CSO with more exposed active sites.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Zhijuan Duan, Yu Ouyang, Yuzhe Fu, Fujian Huang, Fan Xia, Itamar Willner
Summary: In this study, optical and electrochemical probes were introduced for the quantitative assessment of cytochrome c (Cyt. c) in cellular compartments at the single cell level. These probes utilize photoresponsive o-nitrobenzylphosphate ester-caged Cyt. c aptamer constituents, which are uncaged by light stimuli, allowing the spatiotemporal detection of Cyt. c through the formation of Cyt. c/aptamer complexes under apoptotic or non-apoptotic conditions. These probes were applied to distinguish the contents of Cyt. c in cellular compartments of epithelial MCF-10A breast cells and malignant MCF-7 and MDA-MB-231 breast cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Michael P. O'Hagan, Zhijuan Duan, Fujian Huang, Shay Laps, Jiantong Dong, Fan Xia, Itamar Willner
Summary: This review article introduces the mechanisms and applications of photochemically deprotected ONB-functionalized nucleic acids in various research fields. Topics discussed include the synthesis, deprotection mechanisms, and means to tune the irradiation wavelength of ONB-modified nucleic acids. Applications in DNA nanotechnology, materials chemistry, and biological chemistry are highlighted, including sensing, imaging, control of gene expression, and material properties.
Review
Chemistry, Multidisciplinary
Zhenzhen Li, Jianbang Wang, Michael P. O'Hagan, Fujian Huang, Fan Xia, Itamar Willner
Summary: Membrane fusion plays a crucial role in biological transformations and can be mimicked by artificial means using nucleic acids. This article discusses the functionalization of liposomes or membranes with engineered nucleic acids to guide the fusion of cell-like containments, as well as the biophysical and chemical parameters controlling liposome fusion. Membrane fusion processes have various applications in drug delivery, therapeutics, sensing, and biocatalysis.
