Study on Specific Binding Interaction Between Protein and DNA Aptamer via Dynamic Force Spectroscopy

2013 ◽  
Author(s):  
Xiao Ma ◽  
Pranav Shrotriya
Keyword(s):  
Loading Rate ◽  
Specific Binding ◽  
Dna Aptamer ◽  
Dynamic Force ◽  
Binding Interaction ◽  
Force Microscopy ◽  
Bond Breakage ◽  
Coagulation Protein ◽  
Molecular Bond ◽  
Thiolated Aptamer

Recently the need to design nanoscale, sensitive and flexible bio-sensors or biotic-abiotic interface keeps increasing. One of the essential challenges on this objective is to grasp a thorough understanding of the mechanism governing binding interaction between bio-molecules. In this study we aim to demonstrate the binding specificity and reveal force interaction between the anti-coagulation protein thrombin and the single-stranded DNA thrombin aptamer by application of Atomic Force Microscopy (AFM). The thiolated aptamer was deposited onto gold substrate, and then repeatedly brought into contact with a thrombin-coated AFM tip, and force drop-offs during the pull-off were measured to determine the unbinding force between the thrombin-aptamer pair. The results from experiment show that the thrombin-aptamer pair has specific binding and the force between the pair exhibits loading rate dependence. It was shown that the binding forces of the thrombin-aptamer interaction increases with growth of loading rates. The average binding force for a single thrombin/aptamer pair increased from 20 pN to 40 pN, with loading rate changes from 500pN/s to 13500pN/s. Distribution of the unbinding forces measured for each loading rate can be explained on the basis of single energy barrier model for molecular bond breakage.

scholarly journals The force loading rate drives cell mechanosensing through both reinforcement and fluidization

2021 ◽  
Author(s):  
Ion Andreu ◽  
Bryan Falcones ◽  
Sebastian Hurst ◽  
Nimesh Chahare ◽  
Xarxa Quiroga ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Loading Rate ◽  
Dynamic Force ◽  
Force Microscopy ◽  
Loading Rates ◽  
Health And Disease ◽  
Sense And Respond ◽  
Substrate Stretching ◽  
External Forces

AbstractCell response to force regulates essential processes in health and disease. However, the fundamental mechanical variables that cells sense and respond to remain unclear. Here we show that the rate of force application (loading rate) drives mechanosensing, as predicted by a molecular clutch model. By applying dynamic force regimes to cells through substrate stretching, optical tweezers, and atomic force microscopy, we find that increasing loading rates trigger talin-dependent mechanosensing, leading to adhesion growth and reinforcement, and YAP nuclear localization. However, above a given threshold the actin cytoskeleton undergoes fluidization and softens, decreasing loading rates and preventing reinforcement. By stretching rat lungs in vivo, we show that a similar phenomenon occurs at the organ level. Our results show that cell sensing of external forces and of passive mechanical parameters (like tissue stiffness) can be understood through the same mechanisms, driven by the properties under force of the mechanosensing molecules involved.

scholarly journals The force loading rate drives cell mechanosensing through both reinforcement and cytoskeletal softening

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ion Andreu ◽  
Bryan Falcones ◽  
Sebastian Hurst ◽  
Nimesh Chahare ◽  
Xarxa Quiroga ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Loading Rate ◽  
Dynamic Force ◽  
Force Microscopy ◽  
Loading Rates ◽  
Health And Disease ◽  
Sense And Respond ◽  
Substrate Stretching ◽  
External Forces

AbstractCell response to force regulates essential processes in health and disease. However, the fundamental mechanical variables that cells sense and respond to remain unclear. Here we show that the rate of force application (loading rate) drives mechanosensing, as predicted by a molecular clutch model. By applying dynamic force regimes to cells through substrate stretching, optical tweezers, and atomic force microscopy, we find that increasing loading rates trigger talin-dependent mechanosensing, leading to adhesion growth and reinforcement, and YAP nuclear localization. However, above a given threshold the actin cytoskeleton softens, decreasing loading rates and preventing reinforcement. By stretching rat lungs in vivo, we show that a similar phenomenon may occur. Our results show that cell sensing of external forces and of passive mechanical parameters (like tissue stiffness) can be understood through the same mechanisms, driven by the properties under force of the mechanosensing molecules involved.

Crucial Roles of Bond Rebinding in Rupture Behaviors of Single Molecular Bond at Ultralow Loading Rates

2015 ◽  
Vol 07 (01) ◽  
pp. 1550015 ◽  
Author(s):  
Dechang Li ◽  
Baohua Ji
Keyword(s):  
Single Molecule ◽  
Brownian Dynamics ◽  
Loading Rate ◽  
Full Range ◽  
Intrinsic Property ◽  
Dynamic Force ◽  
Mechanical Forces ◽  
Loading Rates ◽  
Molecular Bond

Single-molecule dynamic force spectroscopy (DFS) is a powerful tool for studying mechanical forces of molecular interactions. Recently, the important role of bond rebinding in DSF experiments was recognized, which intrigued mounting researches in this direction. In this work, we study how the bond rebinding influences the strength of single-molecular bonds using Brownian dynamics (BD) simulations and theoretical modeling. Our results show that bond rebinding significantly enhances the strength of single-molecular bond at ultralow loading rates. The rebinding behavior strongly depends on the loading stiffness, suggesting that the strength of single-molecular bond is not only dependent on its intrinsic property, but also the stiffness of loading device. By connecting our new model with conventional theories that did not consider the rebinding effect and are only applied to high loading rates, we propose a unified scheme to predict the rupture forces in a full range of loading rate in DSF experiments and simulations.

Rate dependence of serrated flow in a metallic glass

2003 ◽  
Vol 18 (4) ◽  
pp. 755-757 ◽  
Author(s):  
W. H. Jiang ◽  
M. Atzmon
Keyword(s):  
Plastic Deformation ◽  
Atomic Force Microscopy ◽  
Loading Rate ◽  
Shear Bands ◽  
Shear Band Formation ◽  
Band Formation ◽  
Serrated Flow ◽  
Force Microscopy ◽  
Loading Rates ◽  
Atomic Force

Plastic deformation of amorphous Al90Fe5Gd5 was investigated using nanoindentation and atomic force microscopy. While serrated flow was detected only at high loading rates, shear bands were observed for all loading rates, ranging from 1 to 100 nm/s. However, the details of shear-band formation depend on the loading rate.

Higher Harmonics and Time-Varying Forces in Dynamic Force Microscopy

2010 ◽  
pp. 711-729 ◽  
Author(s):  
Ozgur Sahin ◽  
Calvin F. Quate ◽  
Olav Solgaard ◽  
Franz J. Giessibl
Keyword(s):  
Dynamic Force ◽  
Time Varying ◽  
Higher Harmonics ◽  
Force Microscopy

scholarly journals Sonochemical Reaction of Bifunctional Molecules on Silicon (111) Hydride Surface

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6166
Author(s):  
Serge Ismael Zida ◽  
Yue-Der Lin ◽  
Yit Lung Khung
Keyword(s):  
Photoelectron Spectroscopy ◽  
Lone Pair ◽  
Thermal Reaction ◽  
Silicon Hydride ◽  
Force Microscopy ◽  
Bifunctional Molecules ◽  
Bond Breakage ◽  
Sonochemical Reaction ◽  
Grafting From ◽  
P Type

While the sonochemical grafting of molecules on silicon hydride surface to form stable Si–C bond via hydrosilylation has been previously described, the susceptibility towards nucleophilic functional groups during the sonochemical reaction process remains unclear. In this work, a competitive study between a well-established thermal reaction and sonochemical reaction of nucleophilic molecules (cyclopropylamine and 3-Butyn-1-ol) was performed on p-type silicon hydride (111) surfaces. The nature of surface grafting from these reactions was examined through contact angle measurements, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). Cyclopropylamine, being a sensitive radical clock, did not experience any ring-opening events. This suggested that either the Si–H may not have undergone homolysis as reported previously under sonochemical reaction or that the interaction to the surface hydride via a lone-pair electron coordination bond was reversible during the process. On the other hand, silicon back-bond breakage and subsequent surface roughening were observed for 3-Butyn-1-ol at high-temperature grafting (≈150 °C). Interestingly, the sonochemical reaction did not produce appreciable topographical changes to surfaces at the nano scale and the further XPS analysis may suggest Si–C formation. This indicated that while a sonochemical reaction may be indifferent towards nucleophilic groups, the surface was more reactive towards unsaturated carbons. To the best of the author’s knowledge, this is the first attempt at elucidating the underlying reactivity mechanisms of nucleophilic groups and unsaturated carbon bonds during sonochemical reaction of silicon hydride surfaces.

Nanometre-scale oxidation of silicon surfaces by dynamic force microscopy: reproducibility, kinetics and nanofabrication

1999 ◽  
Vol 10 (1) ◽  
pp. 34-38 ◽  
Author(s):  
M Calleja ◽  
J Anguita ◽  
R Garcia ◽  
K Birkelund ◽  
F Pérez-Murano ◽  
...  
Keyword(s):  
Silicon Surfaces ◽  
Dynamic Force ◽  
Force Microscopy

scholarly journals Detailed studies of the binding mechanism of the Sinorhizobium meliloti transcriptional activator ExpG to DNA

Microbiology ◽  
2005 ◽  
Vol 151 (1) ◽  
pp. 259-268 ◽  
Author(s):  
Birgit Baumgarth ◽  
Frank Wilco Bartels ◽  
Dario Anselmetti ◽  
Anke Becker ◽  
Robert Ros
Keyword(s):  
Binding Site ◽  
Single Molecule ◽  
Sinorhizobium Meliloti ◽  
Specific Binding ◽  
Dna Interaction ◽  
Dynamic Force ◽  
Sequence Motifs ◽  
Promoter Regions ◽  
Dissociation Kinetics ◽  
Direct Binding

The exopolysaccharide galactoglucan promotes the establishment of symbiosis between the nitrogen-fixing Gram-negative soil bacterium Sinorhizobium meliloti 2011 and its host plant alfalfa. The transcriptional regulator ExpG activates expression of galactoglucan biosynthesis genes by direct binding to the expA1, expG/expD1 and expE1 promoter regions. ExpG is a member of the MarR family of regulatory proteins. Analysis of target sequences of an ExpG(His)6 fusion protein in the exp promoter regions resulted in the identification of a binding site composed of a conserved palindromic region and two associated sequence motifs. Association and dissociation kinetics of the specific binding of ExpG(His)6 to this binding site were characterized by standard biochemical methods and by single-molecule spectroscopy based on the atomic force microscope (AFM). Dynamic force spectroscopy indicated a distinct difference in the kinetics between the wild-type binding sequence and two mutated binding sites, leading to a closer understanding of the ExpG–DNA interaction.

Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

2018 ◽  
Vol 97 (5) ◽  
Author(s):  
HongJiang Yang ◽  
Enliang Wang ◽  
WenXiu Dong ◽  
Maomao Gong ◽  
Zhenjie Shen ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Vibrational Mode ◽  
Bond Breakage ◽  
Molecular Bond ◽  
Fragmentation Dynamics

Atomic Force Microscopy

2021 ◽  
pp. 379-400
Author(s):  
C. Julian Chen
Keyword(s):  
Atomic Force Microscopy ◽  
Entire Range ◽  
Tunneling Current ◽  
Vibrational Amplitude ◽  
Dynamic Mode ◽  
Dynamic Force ◽  
Force Detection ◽  
Static Mode ◽  
Force Microscopy ◽  
Atomic Force

This chapter discusses atomic force microscopy (AFM), focusing on the methods for atomic force detection. Although the force detection always requires a cantilever, there are two types of modes: the static mode and the dynamic mode. The general design and the typical method of manufacturing of the cantilevers are discussed. Two popular methods of static force detection are presented. The popular dynamic-force detection method, the tapping mode is described, especially the methods in liquids. The non-contact AFM, which has achieved atomic resolution in the weak attractive force regime, is discussed in detail. An elementary and transparent analysis of the principles, including the frequency shift, the second harmonics, and the average tunneling current, is presented. It requires only Newton’s equation and Fourier analysis, and the final results are analyzed over the entire range of vibrational amplitude. The implementation is briefly discussed.

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