scholarly journals AC Electrokinetics of Polarizable Tri-Axial Ellipsoidal Nano-Antennas and Quantum Dot Manipulation

Micromachines ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 83 ◽  
Author(s):  
Touvia Miloh
Keyword(s):  
Electric Field ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Light Emission ◽  
Weak Field ◽  
Ac Electrokinetics ◽  
Precise Position ◽  
Stagnation Points ◽  
Freely Suspended ◽  
Induced Velocity

By realizing the advantages of using a tri-axial ellipsoidal nano-antenna (NA) surrounded by a solute for enhancing light emission of near-by dye molecules, we analyze the possibility of controlling and manipulating the location of quantum dots (similar to optical tweezers) placed near NA stagnation points, by means of prevalent AC electric forcing techniques. First, we consider the nonlinear electrokinetic problem of a freely suspended, uncharged, polarized ellipsoidal nanoparticle immersed in a symmetric unbounded electrolyte which is subjected to a uniform AC ambient electric field. Under the assumption of small Peclet and Reynolds numbers, thin Debye layer and ‘weak-field', we solve the corresponding electrostatic and hydrodynamic problems. Explicit expressions for the induced velocity, pressure, and vorticity fields in the solute are then found in terms of the Lamé functions by solving the non-homogeneous Stokes equation forced by the Coulombic density term. The particular axisymmetric quadrupole-type flow for a conducting sphere is also found as a limiting case. It is finally demonstrated that stable or equilibrium (saddle-like) positions of a single molecule can indeed be achieved near stagnation points, depending on the directions of the electric forcing and the induced hydrodynamic (electroosmotic) and dielectrophoretic dynamical effects. The precise position of a fluorophore next to an ellipsoidal NA, can thus be simply controlled by adjusting the frequency of the ambient AC electric field.

scholarly journals Optical tweezers in single-molecule biophysics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Carlos J. Bustamante ◽  
Yann R. Chemla ◽  
Shixin Liu ◽  
Michelle D. Wang
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Single Molecule Biophysics

scholarly journals Tuning Single-Molecule Conductance by Controlled Electric Field-Induced trans-to-cis Isomerisation

2021 ◽  
Vol 11 (8) ◽  
pp. 3317
Author(s):  
C.S. Quintans ◽  
Denis Andrienko ◽  
Katrin F. Domke ◽  
Daniel Aravena ◽  
Sangho Koo ◽  
...  
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Single Molecule ◽  
Quantum Interference ◽  
Single Molecule Level ◽  
Wet Chemical Synthesis ◽  
Single Molecule Junctions ◽  
Tunnelling Microscopy ◽  
The Difference

External electric fields (EEFs) have proven to be very efficient in catalysing chemical reactions, even those inaccessible via wet-chemical synthesis. At the single-molecule level, oriented EEFs have been successfully used to promote in situ single-molecule reactions in the absence of chemical catalysts. Here, we elucidate the effect of an EEFs on the structure and conductance of a molecular junction. Employing scanning tunnelling microscopy break junction (STM-BJ) experiments, we form and electrically characterize single-molecule junctions of two tetramethyl carotene isomers. Two discrete conductance signatures show up more prominently at low and high applied voltages which are univocally ascribed to the trans and cis isomers of the carotenoid, respectively. The difference in conductance between both cis-/trans- isomers is in concordance with previous predictions considering π-quantum interference due to the presence of a single gauche defect in the trans isomer. Electronic structure calculations suggest that the electric field polarizes the molecule and mixes the excited states. The mixed states have a (spectroscopically) allowed transition and, therefore, can both promote the cis-isomerization of the molecule and participate in electron transport. Our work opens new routes for the in situ control of isomerisation reactions in single-molecule contacts.

Molecular Motors: Force and Movement Generated by Single Myosin II Molecules

Physiology ◽  
2002 ◽  
Vol 17 (5) ◽  
pp. 213-218 ◽  
Author(s):  
Caspar Rüegg ◽  
Claudia Veigel ◽  
Justin E. Molloy ◽  
Stephan Schmitz ◽  
John C. Sparrow ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Molecular Motors ◽  
Molecular Motor ◽  
Myosin Ii ◽  
Force Production ◽  
Myosin Isoforms ◽  
Single Molecule Level ◽  
Recent Developments ◽  
Muscle Myosin

Muscle myosin II is an ATP-driven, actin-based molecular motor. Recent developments in optical tweezers technology have made it possible to study movement and force production on the single-molecule level and to find out how different myosin isoforms may have adapted to their specific physiological roles.

scholarly journals Single-molecule force spectroscopy reveals folding steps associated with hormone binding and activation of the glucocorticoid receptor

2018 ◽  
Vol 115 (46) ◽  
pp. 11688-11693 ◽  
Author(s):  
Thomas Suren ◽  
Daniel Rutz ◽  
Patrick Mößmer ◽  
Ulrich Merkel ◽  
Johannes Buchner ◽  
...  
Keyword(s):  
Free Energy ◽  
Glucocorticoid Receptor ◽  
Ligand Binding ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Mechanical Load ◽  
Force Spectroscopy ◽  
Folding Pathway ◽  
Hormone Binding ◽  
Single Molecule Force Spectroscopy

The glucocorticoid receptor (GR) is a prominent nuclear receptor linked to a variety of diseases and an important drug target. Binding of hormone to its ligand binding domain (GR-LBD) is the key activation step to induce signaling. This process is tightly regulated by the molecular chaperones Hsp70 and Hsp90 in vivo. Despite its importance, little is known about GR-LBD folding, the ligand binding pathway, or the requirement for chaperone regulation. In this study, we have used single-molecule force spectroscopy by optical tweezers to unravel the dynamics of the complete pathway of folding and hormone binding of GR-LBD. We identified a “lid” structure whose opening and closing is tightly coupled to hormone binding. This lid is located at the N terminus without direct contacts to the hormone. Under mechanical load, apo-GR-LBD folds stably and readily without the need of chaperones with a folding free energy of 41 kBT (24 kcal/mol). The folding pathway is largely independent of the presence of hormone. Hormone binds only in the last step and lid closure adds an additional 12 kBT of free energy, drastically increasing the affinity. However, mechanical double-jump experiments reveal that, at zero force, GR-LBD folding is severely hampered by misfolding, slowing it to less than 1·s−1. From the force dependence of the folding rates, we conclude that the misfolding occurs late in the folding pathway. These features are important cornerstones for understanding GR activation and its tight regulation by chaperones.

Single-molecule transistors

2015 ◽  
Vol 44 (4) ◽  
pp. 902-919 ◽  
Author(s):  
Mickael L. Perrin ◽  
Enrique Burzurí ◽  
Herre S. J. van der Zant
Keyword(s):  
Electric Field ◽  
Single Molecule ◽  
Gate Electrode ◽  
Single Molecule Transistor

Artist impression of a single-molecule transistor, where a molecule is connected to the source and the drain electrodes. The red lines illustrated the electric field caused by the gate electrode, located below.

scholarly journals Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sean P. Carney ◽  
Wen Ma ◽  
Kevin D. Whitley ◽  
Haifeng Jia ◽  
Timothy M. Lohman ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Atp Hydrolysis ◽  
Variable Number ◽  
Structural Basis ◽  
Variable Step Size ◽  
Dna Unwinding ◽  
Step Size ◽  
Structural Mechanism ◽  
Dynamics Simulations

AbstractUvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. Previous estimates of its step size have been indirect, and a consensus on its stepping mechanism is lacking. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hexameric helicases.

scholarly journals Ripping RNA by Force using Gaussian Network Models

2016 ◽  
Author(s):  
Changbong Hyeon ◽  
D. Thirumalai
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Cross Correlation ◽  
Network Models ◽  
Force Extension ◽  
Correlation Matrices ◽  
Rna Molecules ◽  
Allosteric Communication ◽  
Ion Effects ◽  
Gaussian Network

AbstractUsing force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in the context of proteins have shown that topology plays is the major determinant of the unfolding landscapes. By building on this finding we study the responses of RNA molecules to force by adapting Gaussian network model (GNM) that represents RNAs using a bead-spring network with isotropic interactions. Cross-correlation matrices of residue fluctuations, which are analytically calculated using GNM even upon application of mechanical force, show distinct allosteric communication as RNAs rupture. The model is used to calculate the force-extension curves at full thermodynamic equilibrium, and the corresponding unfolding pathways of four RNA molecules subject to a quasi-statically increased force. Our study finds that the analysis using GNM captures qualitatively the unfolding pathway of T. ribozyme elucidated by the optical tweezers measurement. However, the simple model is not sufficient to capture subtle features, such as bifurcation in the unfolding pathways or the ion effects, in the forced-unfolding of RNAs.

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