Article
Biochemical Research Methods
Annelies Dillen, Wouter Vandezande, Devin Daems, Jeroen Lammertyn
Summary: Duplexed aptamers (DAs) are aptasensor formats that can simultaneously recognize and signal the concentration of target molecules, consisting of an aptamer and an aptamer complementary element (ACE). However, the tailored development of DAs for a particular target is currently based on trial and error due to limited knowledge about how the ACE sequence affects the final performance of the biosensors.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Guan-Yu Qiao, Dehui Guan, Shuai Yuan, Heng Rao, Xiao Chen, Jia-Ao Wang, Jun-Sheng Qin, Ji-Jing Xu, Jihong Yu
Summary: Encapsulating CsPbBr3 nanocrystals into a stable metal-organic framework greatly enhances their photocatalytic performance, with significant charge transfer observed at the interface between the quantum dots and the MOF. This composite material shows excellent catalytic activity in oxygen reduction and evolution reactions, as well as serving as a synergistic photocathode in Li-O-2 batteries, highlighting the cooperative effect between CsPbBr3 and PCN-333(Fe).
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Physics, Fluids & Plasmas
Ting Liang, Chao Yang, Xiaoya Song, Yuyu Feng, Yanhui Liu, Hu Chen
Summary: This study systematically investigated the kinetics and thermodynamics of the folding-unfolding transition of an individual DNA hairpin in a crowded environment using a combination of high-resolution magnetic tweezers and an extended crowder-oxDNA model. The results demonstrated a linear dependence of the critical force of the DNA hairpin on the polyethylene glycol (PEG) concentration, highlighting the importance of excluded volume effects in the interaction between PEG and the DNA hairpin. The method provides insights into accurately mimicking cytosolic environments using mixtures of different inert molecules. Overall rating: 9/10.
Article
Multidisciplinary Sciences
Alex M. Yoshikawa, Alexandra E. Rangel, Liwei Zheng, Leighton Wan, Linus A. Hein, Amani A. Hariri, Michael Eisenstein, H. Tom Soh
Summary: Aptamer-based molecular switches have various applications such as imaging metabolites, drug delivery, and biomolecule detection. Conventional aptamer selection methods do not produce aptamers with structure-switching functionality, so post-selection modification is necessary. This study presents a screening-based strategy that can convert any aptamer into a molecular switch without prior knowledge of its structure.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Saanfor Hubert Suh, Yongzheng Xing, Alexia Rottensteiner, Rong Zhu, Yoo Jin Oh, Stefan Howorka, Peter Hinterdorfer
Summary: This study investigates molecular recognition in a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions. The results show that the association rates are slower and the dissociation rates are faster for receptors positioned deeper inside the pore lumen. This phenomenon can be explained by the steric constraints on molecular interactions in confinement.
Article
Chemistry, Applied
Aloys Hitabatuma, Yue-hong Pang, Li-hong Yu, Xiao-fang Shen
Summary: An ultrasensitive method for rapid and specific detection of Ochratoxin A (OTA) was designed using complementary sequence to aptamer as a target of molecular beacons. The method showed linear increase in fluorescence intensity with OTA concentration and a detection limit of 0.247 pg mL(-1), making it a potential sensing platform for OTA detection in wheat samples when compared to traditional HPLC-MS/MS method.
Article
Chemistry, Physical
Yi Ji, Zhengmao Liu, Zhenchao Zhao, Pan Gao, Xinhe Bao, Kuizhi Chen, Guangjin Hou
Summary: The study investigates the molecular dynamics of molecules in MFI zeolites and finds that the structural differences have a significant impact on shape selectivity. In the absence of acid sites, molecules can only diffuse along straight channels and tend to occupy channel intersections. Different types of pore confinements result in different dynamic motions of the molecules. With the presence of acid sites, molecules are strongly adsorbed and their motions are further impeded.
Article
Multidisciplinary Sciences
Qian Wang, Jie Yang, Zhicheng Zhong, Jeffrey A. Vanegas, Xue Gao, Anatoly B. Kolomeisky
Summary: This study introduces general principles for editor design to reduce bystander effects, which are successfully applied to new mutations that effectively reduce bystander editing at different genomic loci.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Hsuan-Lei Sung, David J. Nesbitt
Summary: The conformational dynamics of riboswitches, including ligand binding and RNA folding, are influenced by excluded volume effects under crowded cellular conditions. This study investigates how the molecular crowder PEG affects the folding of the B. subtilis LysC lysine riboswitch using single molecule FRET spectroscopy. The results show that PEG crowding facilitates riboswitch folding by increasing the affinity for the cognate ligand, and this effect is not purely entropic but also impacts the enthalpic contributions to the folding free energy landscape.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Isabella DeStefano, Gabriella DeStefano, Nicholas J. Paradis, Roshani Patel, Austin K. Clark, Hunter Gogoj, Gurvir Singh, Keertana S. Jonnalagadda, Aashka Y. Patel, Chun Wu, Gregory A. Caputo, Timothy D. Vaden
Summary: The study investigated the thermal unfolding of the copper redox protein azurin in the presence of four different amino acid-based ionic liquids (ILs), showing that these ILs destabilize the protein structure and decrease its melting temperature. ILs with alcohol side chains have a stronger impact on protein stability, while those with acidic side chains have weaker effects.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biophysics
Luana Barbosa Correa, Suyene Rocha Pinto, Luciana Magalhaes Rebelo Alencar, Sotiris Missailidis, Elaine Cruz Rosas, Maria das Gracas Muller de Oliveira Henriques, Ralph Santos-Oliveira
Summary: A nanoaptamer anti-MUC1/Y was developed and evaluated as a nanoagent for rheumatoid arthritis treatment, showing high entrapment efficacy and significant therapeutic effects, especially at low doses. The results confirm the applicability of this nanosystem for RA treatment.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Chemistry, Analytical
Chao Wang, Kexiao Zhu, Jie Yu, Pengfei Shi
Summary: This paper presents an improved molecular beacon method for the rapid and sensitive detection of aflatoxin B1 (AFB1), a highly carcinogenic natural mycotoxin. The molecular beacon, consisting of a DNA aptamer flanked by FAM and BHQ1, showed a larger fluorescent response to AFB1 with the assistance of complementary DNA (cDNA) chain. By optimizing key experimental factors, the method achieved rapid detection of AFB1 within 20 minutes in a concentration range of 1 nM to 3 μM. The aptamer-based molecular beacon method demonstrated easy operation, rapid analysis, larger signal response, good specificity, anti-interference ability, and potential for real-sample analysis.
Article
Chemistry, Physical
Linlin Tang, Mengjiao Huang, Mingjiao Zhang, Yufeng Pei, Yan Liu, Yong Wei, Chaoyong Yang, Teng Xie, Dong Zhang, Ruhong Zhou, Yanling Song, Jie Song
Summary: Multivalent interactions enhance the binding efficiency of ligands to target molecules. A direct SELEX strategy using a preorganized DNA framework library was developed to select an antibody-mimicking multivalent aptamer (Amap) for epithelial cell adhesion molecule (EpCAM). Amap exhibits good binding affinity through both aptamer moieties binding to EpCAM simultaneously, and this strategy has the potential to be a new route for de novo evolution of multivalent aptamers.
Article
Nanoscience & Nanotechnology
Madhu Biyani, Kaori Yasuda, Yasuhiro Isogai, Yuki Okamoto, Wei Weilin, Noriyuki Kodera, Holger Flechsig, Toshiyuki Sakaki, Miki Nakajima, Manish Biyani
Summary: A novel DNA aptamer-based CYP24 inhibitor was identified, which showed selective inhibition of CYP24 with high affinity and induced antiproliferative activity in cancer cells. This aptamer provides a new approach for tumor diagnosis and treatment.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Xiang Guo, Pengfei Li, Guoming Liu, Ye Tian, Zongbo Zhang, Caihong Xu, Lei Jiang
Summary: This study demonstrates a new strategy to construct inorganic-organic nanocomposites by dispersing nano-phased polymer in consecutive inorganic matrix via covalent bonds. The resulting nanocomposites exhibit enhanced thermal stability and combine the characteristics of both inorganic and organic materials.
Article
Chemistry, Multidisciplinary
Cuiping Mao, Shuchen Wang, Jiankai Li, Zhuowei Feng, Tong Zhang, Rui Wang, Chunhai Fan, Xingyu Jiang
Summary: DNA, as a storage medium, offers high information density but requires specialized equipment and controlled environments. We introduce a DNA microlibrary encapsulated in metal-organic frameworks (MOFs) within 10 minutes and extracted in 5 minutes using a microfluidic chip for automated and integrated DNA-based data storage. The DNA microlibrary@MOFs enhances the stability of data-encoded DNA against harsh environments and can be read out perfectly after accelerated aging, equivalent to 10-year storage under specific conditions.
Article
Chemistry, Multidisciplinary
Qiao Zhang, Kai Xia, Meng Jiang, Qingting Li, Weigang Chen, Mingzhe Han, Wei Li, Rongqin Ke, Fei Wang, Yongxing Zhao, Yuehua Liu, Chunhai Fan, Hongzhou Gu
Summary: This study presents a new method called PECAN (paired-end cutting assisted by DNAzymes), which allows for the mass production of high-quality single-stranded DNA with arbitrary sequences. The method utilizes self-hydrolyzing DNAzymes to generate precursor DNA, which can then be amplified and processed to release large quantities of target DNA. PECAN offers high customizability, purity, and scalability, making it suitable for a wide range of applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Zhichao Liu, Ying Zhu, Liming Zhang, Weiping Jiang, Yawei Liu, Qiaowei Tang, Xiaoqing Cai, Jiang Li, Lihua Wang, Changlu Tao, Xianzhen Yin, Xiaowei Li, Shangguo Hou, Dawei Jiang, Kai Liu, Xin Zhou, Hongjie Zhang, Maili Liu, Chunhai Fan, Yang Tian
Summary: Analyzing the complex structures and functions of the brain is crucial for understanding physiological and pathological processes. However, subcellular structures of cells in the live brain and the concentrations, distributions, and interactions of functional molecules are still poorly understood.
SCIENCE CHINA-CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Xinxin Jing, Yueyue Zhang, Min Li, Xiaolei Zuo, Chunhai Fan, Junhua Zheng
Summary: Synthesis of engineered colloidal nanoparticles with delicate surface characteristics contributes to multifunctional applications. Surface engineering methods, including grafting suitable molecules or macromolecules, have been developed to improve stability and enable programmable assembly of nanoparticles.
MATERIALS HORIZONS
(2023)
Article
Nanoscience & Nanotechnology
Fangfei Yin, Haipei Zhao, Shasha Lu, Juwen Shen, Min Li, Xiuhai Mao, Fan Li, Jiye Shi, Jiang Li, Baijun Dong, Wei Xue, Xiaolei Zuo, Xiurong Yang, Chunhai Fan
Summary: The article introduces a DNA-encoded molecular classifier that can classify multidimensional molecular clinical data and has been tested in prostate cancer patients.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Meiyuan Qi, Wenhe Ma, Qin Xu, Fei Wang, Ping Song, Sisi Jia, Xiaolei Zuo, Mingqiang Li, Guangbao Yao, Chunhai Fan
Summary: Dynamic molecular interactions in chemical reaction networks lead to complex behaviors in living systems. Programming DNA molecular reactions at molecular and nanometer scales have been achieved, but achieving programmable autonomous behavior at submicron or larger scales remains challenging. This study presents a mechanism of meta-DNA strand displacement reactions (M-SDRs) mediated solely by meta-toehold (M-toehold) using versatile submicron building blocks of meta-DNA (M-DNA). M-SDR emulates the toehold binding and branch migration processes and shows potential for programming autonomous behavior at the cellular level.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Kun Dai, Yang Xu, Yang Yang, Jianfeng Shen, Xiaoguo Liu, Xinyi Tu, Lu Yu, Xiaodong Qi, Jiang Li, Lihua Wang, Xiaolei Zuo, Yingbin Liu, Hao Yan, Chunhai Fan, Guangbao Yao
Summary: This study utilizes single-stranded RNA (ssRNA) origami as ligands for nucleic acid-sensing receptors, achieving improved stability, targeting, and immunogenicity prediction. The ssRNA self-folds into compact nanoparticles with defined shapes and exhibits resistance against degradation in cells. It can activate macrophages and neutrophils in the tumor microenvironment, leading to anti-tumoral immune response and tumor growth retardation in a mouse model. This ssRNA origami strategy provides a new solution for ligand design and biomedical applications of nucleic acid sensors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Hui Lv, Nuli Xie, Mingqiang Li, Mingkai Dong, Chenyun Sun, Qian Zhang, Lei Zhao, Jiang Li, Xiaolei Zuo, Haibo Chen, Fei Wang, Chunhai Fan
Summary: We demonstrate a general-purpose DNA integrated circuit (DIC) system by integrating multilayer DNA-based programmable gate arrays (DPGAs), which can be reconfigured and programmed to implement a wide range of circuits. We also show that DNA origami registers can control the asynchronous execution of cascaded DPGAs, and the integration of a DPGA with an analog-to-digital converter can be used for disease classification.
Article
Computer Science, Artificial Intelligence
Yan Zhao, Shuting Cao, Yue Wang, Fan Li, Lixuan Lin, Linjie Guo, Fei Wang, Jie Chao, Xiaolei Zuo, Ying Zhu, Lihua Wang, Jiang Li, Chunhai Fan
Summary: The environments in living cells are highly heterogeneous and compartmentalized, posing a grand challenge for the deployment of theranostic agents with spatiotemporal precision. Despite rapid advancements in creating nanodevices responsive to various cues in cellular environments, it remains difficult to control their operations based on the temporal sequence of these cues.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Multidisciplinary Sciences
Tingting Zhai, Yuhan Wei, Lihua Wang, Jiang Li, Chunhai Fan
Summary: Airborne diseases such as SARS, bird flu, and COVID-19 have increased the need for novel bioassay methods for early-stage diagnosis and large-scale screening. This article summarizes the latest methods for detecting infectious pathogens and discusses key challenges. It highlights the trend towards next-generation technologies that utilize advancements in microfabrication, nanotechnology, and synthetic biology to enable sensitive, rapid, and affordable pathogen assays with portable intelligent devices.
FUNDAMENTAL RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Longyi Zhu, Yiting Shen, Shengyuan Deng, Ying Wan, Jun Luo, Yan Su, Mingxu You, Chunhai Fan, Kewei Ren
Summary: Researchers have developed a synthetic DNA binder that can induce mitochondrial aggregation and fusion in living cells. This DNA binder has shown potential for repairing ROS-stressed neuron cells and can be further customized to achieve stimuli-triggered mitochondrial aggregation and fusion. The researchers believe that this new DNA regulator system can be a powerful tool for subcellular manipulation and precision therapy.
Article
Chemistry, Multidisciplinary
Yao Luo, Min Yin, Chunlan Mu, Xingjie Hu, Hui Xie, Jingyi Li, Tingting Cao, Nan Chen, Ji Wu, Chunhai Fan
Summary: This study developed a nanocomplex, Pdot-siRNA, based on semiconductor polymer dots for effective gene knockdown in female germline stem cells (FGSCs). The high fluorescence brightness of Pdots was utilized for comprehensive investigation of their cellular uptake, intracellular trafficking, and exocytosis in FGSCs. Furthermore, Pdots demonstrated excellent biocompatibility and minimal disturbance to FGSCs differentiation. The intracellular Pdots could escape from lysosomes and undergo active exocytosis, making them ideal nanocarriers for bioactive cargos. Additionally, Pdot-siRNA could penetrate into 3D ovarian organoids derived from FGSCs and down-regulate the expression levels of target genes. This study sheds light on the manipulation and medical application of FGSCs and explores the interface between theranostic nanoparticles and FGSCs for the first time.
ADVANCED MATERIALS
(2023)
Review
Biochemical Research Methods
Yuan Luo, Zhen Cao, Yifan Liu, Rong Zhang, Shijia Yang, Ning Wang, Qingyuan Shi, Jie Li, Shurong Dong, Chunhai Fan, Jianlong Zhao
Summary: DNA has shown great potential as an alternative for digital information storage but is currently hindered by high material cost, time consumption for data reading/writing, and lack of an integrated system. Microfluidics has emerged as a promising solution because of its ability to handle and process micro-scale fluid samples in a highly integrated manner. This review discusses recent efforts and advancements in applying microfluidics to DNA data storage, highlighting its potential and future directions for integration and real-life applications.
Article
Biotechnology & Applied Microbiology
Kaidi Wang, Jing Chen, Jay Martiniuk, Xiangyun Ma, Qifeng Li, Vivien Measday, Xiaonan Lu
Summary: Reliable typing of yeast strains is crucial for the alcoholic beverage industry, and this study proposes a method using Raman spectroscopy and CNN for species identification and strain discrimination of S. cerevisiae and S. uvarum. The results demonstrate high accuracy and fast speed, providing significant implications for improving the quality of fermented beverages and conducting high-throughput screening.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)