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Chinese Physics B 2021年第7期30卷 595-599页

作者： Huanhuan Su Hao Sun Haiyan Hong Zilong Guo Ping Yu Hu Chen Institute for Biomimetics and Soft Matter Fujian Provincial Key Laboratory for Soft Functional Materials ResearchDepartment of PhysicsXiamen UniversityXiamen 361005China Center of Biomedical Physics Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou 325000China Oujiang Laboratory Wenzhou 325000China

Src SH3 protein domain is a typical two-state protein which has been confirmed by research of denaturant-induced unfolding *** spectroscopy experiments by optical tweezers and atomic force microscopy have measured the force-dependent unfolding rates with different kinds of pulling ***,the equilibrium folding and unfolding dynamics at constant forces has not been ***,using stable magnetic tweezers,we performed equilibrium folding and unfolding dynamic measurement and force-jump measurement of src SH3 domain with tethering points at its N-and *** the obtained force-dependent transition rates,a detailed two-state free energy landscape of src SH3 protein is constructed with quantitative information of folding free energy,transition state barrier height and position,which exemplifies the capability of magnetic tweezers to study protein folding and unfolding dynamics.

关键词： protein folding and unfolding magnetic tweezers free energy landscape transition state

Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers

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Biophysics Reports 2018年第4期4卷 222-232页

作者： Xue Xiao Liping Dong Yi-Zhou Wang Peng-Ye Wang Ming Li Guohong Li Ping Chen Wei Li National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics Institute of PhysicsChinese Academy of Sciences University of Chinese Academy of Sciences National Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences

The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on singlemolecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression.

关键词： Chromatin fiber Dynamics magnetic tweezers Single molecule

Mutation in a non-force-bearing region of protein L influences force-dependent unfolding behavior

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Chinese Physics B 2024年第7期33卷 624-629页

作者：蒋环杰王艳伟陈家媛胡丹潘海郭子龙陈虎 Department of Physics Wenzhou UniversityWenzhou 325035China Center of Biomedical Physics Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou 325000China Research Institute for Biomimetics and Soft Matter Fujian Provincial Key Laboratory for Soft Functional Materials ResearchDepartment of PhysicsXiamen UniversityXiamen 361005China

Single-molecule magnetic tweezers(MTs) have revealed multiple transition barriers along the unfolding pathway of several two-state proteins, such as GB1 and Csp. In this study, we utilized MTs to measure the force-dependent folding and unfolding rates of both protein L(PLWT) and its Y47W mutant(PLY47W) where the mutation point is not at the force-bearing β-strands. The measurements were conducted within a force range of 3–120 pN. Notably, the unfolding rates of both PLWT and PWY47W exhibit distinct force sensitivities below 50 pN and above 60 pN, implying a two-barrier free energy landscape. Both PLWT and PLY47W share the same force-dependent folding rate and the same transition barriers,but the unfolding rate of PLY47W is faster than that of PLWT. Our finding demonstrates that the residue outside of the force-bearing region will also affect the force-induced unfolding dynamics.

关键词： protein folding magnetic tweezers protein L

Reading Time and DNA Sequence Preference of TET3 CXXC Domain Revealed by Single-Molecule Profiling

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Chinese Journal of Chemistry 2023年第10期41卷 1177-1184页

作者： Zeyu Wang Zhiqiang Cao Kangkang Ma Man Lu Meije Wang Han Gao Deshun Gong Lin Liang Zhongbo Yu Frontiers Science Center for Cell Responses State Key Laboratory of Medicinal Chemical Biologyand College of PharmacyNankai University38 Tongyan RoadTianjin 300350China State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences Nankai UniversityTianjin 300350China College of Animal Science Shanxi Agricultural UniversityTaiguShanxi 030801China

Recognition of CpG dinucleotide DNA in epigenetic information flow plays a pivotal role for cellular differentiation and *** TET3 CXXC domain binds to CpG DNA,serving a basic epigenetic information reading *** the selective recognition of a CpG motif by a CXXC domain from crowded binding sites in a gene sequence,the protein-DNA interactions are beyond CpG ***,the selective binding dynamics of CpG within a long DNA context by epigenetic enzymes have been rarely exploit-ed,which is hard for ensemble methods to ***,we used single-molecule magnetic tweezers to quantitatively examine the dynamics of TET3's CXXC domain on a Hoxa9 promoter *** single-molecule binding profile revealed that CXXC-DNA interactions involve both CpG motifs and their flanking *** residence time of TET3 CXXC differs by about 1000 times in five distin-guished CpG clusters in the context of a CpG ***,we performed multi-state hidden Markov modeling analysis on the zip-ping/unzipping dynamics of a CpG hairpin,discovering TET3 CXXC's preference on CpG motifs regarding the-2 to+2 flanking *** results shed light on the selective binding dynamics of a CXXC on a gene sequence,facilitating studies on epigenetic information reading mechanisms.

关键词： Enzymes DNA recognition CpG flanking sequence Single-molecule studies magnetic tweezers

Theoretical study of the nonlinear force-loading control in single-molecule stretching experiments

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Communications in Theoretical Physics 2024年第4期76卷 167-175页

作者： Xingyu Qi Zilong Guo Shimin Le Hu Chen Research Institute for Biomimetics and Soft Matter Fujian Provincial Key Lab for Soft Functional Materials ResearchDepartment of PhysicsXiamen UniversityXiamen 361005China Center of Biomedical Physics Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou 325000China

Force spectrum measurements with constant loading rates are widely used in single-molecule manipulation experiments to study the mechanical stability and force response of ***-dependent transition rates can be obtained from the transition force distribution,but it is limited to the force range with non-zero force *** constant loading rate control can be realized with magnetic tweezers,the loading rate range is limited due to the slow movement of permanent ***-linear exponential and exponential squared force loading functions are more feasible in magnetic tweezers,while there is no theoretical result available for these two kinds of non-linear force loading *** this study,we solved the unfolding process of a protein following Bell's model under nonlinear exponential and exponential squared force loading functions,which offer a broader range of unfolding force distribution compared to the traditional constant loading rate ***,we derived two force loading functions,which can produce uniform unfolding force *** research contributes fundamental equations for the analysis of experimental data obtained through single-molecule manipulation under nonlinear force loading controls,paving the way for the use of nonlinear force control in magnetic tweezer experiments.

关键词： single-molecule manipulation magnetic tweezers force loading transition rates force distribution

A multi-field approach to DNA condensation

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Chinese Physics B 2015年第12期24卷 28-37页

作者：冉诗勇贾俊丽 Department of Physics Wenzhou University

DNA condensation is an important process in many fields including life sciences, polymer physics, and applied technology. In the nucleus, DNA is condensed into chromosomes. In polymer physics, DNA is treated as a semi-flexible molecule and a polyelectrolyte. Many agents, including multi-valent cations, surfactants, and neutral poor solvents, can cause DNA condensation, also referred to as coil–globule transition. Moreover, DNA condensation has been used for extraction and gene delivery in applied technology. Many physical theories have been presented to elucidate the mechanism underlying DNA condensation, including the counterion correlation theory, the electrostatic zipper theory, and the hydration force theory. Recently several single-molecule studies have focused on DNA condensation, shedding new light on old concepts. In this document, the multi-field concepts and theories related to DNA condensation are introduced and clarified as well as the advances and considerations of single-molecule DNA condensation experiments are introduced.

关键词： DNA condensation coil–globule transition polyelectrolyte Manning theory counterion correlation hydration force single-molecule magnetic tweezers

Catch-bond behavior of DNA condensate under tension

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Chinese Physics B 2015年第12期24卷 105-108页

作者：李伟 Wong Wei-Juan Lim Ci-Ji 车海鹏李明严洁王鹏业 Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Department of Physics National University of Singapore Singapore 117542and Mechanobiology Institute National University of Singapore

Toroid formation is an important mechanism underlying DNA condensation, which has been investigated extensively by single-molecule experiments in vitro. Here, the de-condensation dynamics of DNA condensates were studied using magnetic tweezers combined with Brownian dynamics simulations. The experimental results revealed a surprising nonmonotonic dependence of the unfolding rate on the force applied under strong adhesion conditions, resembling the catchbond behavior reported in the field of ligand-receptor interactions. Simulation results showed that the different unfolding pathways of DNA condensate under large forces derive from the force-dependent deformation of the DNA toroid, which explains the catch-bond behavior of DNA condensate in the magnetic tweezers experiments. These results challenge the universality of the regular toroidal DNA unwrapping mechanism and provide the most complete description to date of multivalent cation-dependent DNA unwrapping under tension.

关键词： DNA toroid magnetic tweezers catch bond

Unfolding rates of 1:1 and 2:1 complex of CX-5461 and c-MYC promoter G-quadruplexes revealed by single-molecule force spectroscopy

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Biophysics Reports 2024年第3期10卷 180-189页

作者： Hui Peng Yashuo Zhang Qun Luo Xinyu Wang Huijuan You Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology College of Physics Science and Technology Yangzhou University

CX-5461, also known as pidnarulex, is a strong G4 stabilizer and has received FDA fast-track designation for BRCA1-and BRCA2-mutated cancers. However, quantitative measurements of the unfolding rates of CX-5461-G4 complexes which are important for the regulation function of G4s, remain ***, we employ single-molecule magnetic tweezers to measure the unfolding force distributions of c-MYC G4s in the presence of different concentrations of CX-5461. The unfolding force distributions exhibit three discrete levels of unfolding force peaks, corresponding to three binding modes. In combination with a fluorescent quenching assay and molecular docking to previously reported ligand-c-MYC G4 structure, we assigned the ～69 pN peak corresponding to the 1:1（ligand:G4） complex where CX-5461binds at the G4's 5'-end. The ～84 p N peak is attributed to the 2:1 complex where CX-5461 occupies both the 5' and 3'. Furthermore, using the Bell-Arrhenius model to fit the unfolding force distributions,we determined the zero-force unfolding rates of 1:1, and 2:1 complexes to be（2.4 ± 0.9） × 10-8s-1and（1.4 ± 1.0） × 10-9s-1respectively. These findings provide valuable insights for the development of G4-targeted ligands to combat c-MYC-driven cancers.

关键词： Single-molecule G-quadruplex magnetic tweezers Stoichiometry Force spectroscopy Pidnarulex

DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules

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Biophysics Reports 2022年第4期8卷 212-224页

作者： Xiaodan Zhao Xuyao Priscilla Liu Jie Yan Department of Physics National University of Singapore Centre for Bioimaging Sciences National University of Singapore Mechanobiology Institute National University of Singapore

The functions of DNA-binding proteins are dependent on protein-induced DNA distortion, the binding preference to special sequences, DNA secondary structures, the binding kinetics and the binding affinity. Recent rapid progress in single-molecule imaging and mechanical manipulation technologies have made it possible to directly probe the DNA binding by proteins, footprint the positions of the bound proteins on DNA, quantify the kinetics and the affinity of protein–DNA interactions, and study the interplay of protein binding with DNA conformation and DNA topology. Here, we review the applications of an integrated approach where the single-DNA imaging using atomic force microscopy and the mechanical manipulation of single DNA molecules are combined to study the DNA–protein interactions. We also provide our views on how these findings yield new insights into understanding the roles of several essential DNA architectural proteins.

关键词： AFM imaging Single-molecule manipulation magnetic tweezers Optical tweezers DNA–protein interactions DNA supercoiling DNA distortion