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

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 biomolecules.Force-dependent transition rates can be obtained from the transition force distribution,but it is limited to the force range with non-zero force distribution.Although constant loading rate control can be realized with magnetic tweezers,the loading rate range is limited due to the slow movement of permanent magnets.Non-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 functions.In 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 experiments.Furthermore,we derived two force loading functions,which can produce uniform unfolding force distribution.This 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

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Understanding the physics of DNA using nanoscale single-molecule manipulation

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Frontiers in Biology 2012年第5期7卷 576-581页

作者： Eric W. Frey Ashton A. Gooding Sitara Wijeratne Ching-Hwa Kiang Department of Physics and Astronomy Rice University Houston TX 77005 USA

Processes for decoding the genetic information in cells, including transcription, replication, recombi- nation and repair, involve the deformation of DNA from its equilibrium structures such as bending, stretching, twisting, and unzipping of the double helix. single-molecule manipulation techniques have made it possible to control DNA conformation and simultaneously detect the induced changes, revealing a rich variety of mechanically-induced conformational changes and thermodynamic states. These single-molecule techniques helped us to reveal the physics of DNA and the processes involved in the passing on of the genetic code.

关键词： single-molecule manipulation the physics of DNA

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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

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manipulation and control of a single molecular rotor on Au(111) surface

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Chinese Physics B 2010年第1期19卷 538-543页

作者：张海刚毛金海刘奇江楠周海涛郭海明时东霞高鸿钧 Beijing National Laboratory of Condensed Matter Physics Institute of PhysicsChinese Academy of Sciences

Three different methods are used to manipulate and control phthalocyanine based single molecular rotors on Au （111） surface：（1） changing the molecular structure to alter the rotation potential; （2） using the tunnelling current of the scanning tunnelling microscope （STM） to change the thermal equilibrium of the molecular rotor; （3） artificial manipulation of the molecular rotor to switch the rotation on or off by an STM tip. Furthermore, a molecular ＇gear wheel＇ is successfully achieved with two neighbouring molecules.

关键词： single molecular rotor scanning tunnelling microscope single-molecule manipulation

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