A Single Molecule Level Study of the Temperature-Dependent Kinetics for the Formation of Metal Porphyrin Monolayers on Au(111) from Solution

2014 ◽  
Vol 136 (5) ◽  
pp. 2142-2148 ◽  
Author(s):  
Ashish Bhattarai ◽  
Ursula Mazur ◽  
K. W. Hipps
Keyword(s):  
Single Molecule ◽  
Temperature Dependent ◽  
Metal Porphyrin ◽  
Single Molecule Level

Single molecule level studies of reversible ligand binding to metal porphyrins at the solution/solid interface

2020 ◽  
Vol 24 (08) ◽  
pp. 993-1002 ◽  
Author(s):  
Ursula Mazur ◽  
K. W. Hipps
Keyword(s):  
Ligand Binding ◽  
Single Molecule ◽  
Quantitative Information ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Metal Porphyrin ◽  
Single Molecule Level ◽  
Solid Interface ◽  
Metal Porphyrins ◽  
Exogenous Ligands

Ligands bind reversibly to metal porphyrins in processes such as molecular recognition, electron transport and catalysis. These chemically relevant processes are ubiquitous in biology and are important in technological applications. In this article, we focus on the current advances in ligand binding to metal porphyrin receptors noncovalently bound at the solution/solid interface. In particular, we restrict ourselves to studies at the single molecule level. Dynamics of the binding/dissociation process can be monitored by scanning tunneling microscopy (STM) and can yield both qualitative and quantitative information about ligand binding affinity and the energetics that define a particular ligation reaction. Molecular and time dependent imaging can establish whether the process under study is at equilibrium. Ligand-concentration-dependent studies have been used to determine adsorption isotherms and thermodynamic data for processes occurring at the solution/solid interface. In several binding reactions, the solid support acted as an electron-donating fifth coordination site, thereby significantly changing the metal porphyrin receptor’s affinity for exogenous ligands. Supporting calculations provide insight into the metalloporphyrin/support and ligand–metalloporphyrin/support interactions and their energetics.

Polypeptide Translocation Through the Mitochondrial TOM Channel: Temperature-Dependent Rates at the Single-Molecule Level

2012 ◽  
Vol 4 (1) ◽  
pp. 78-82 ◽  
Author(s):  
Kozhinjampara R. Mahendran ◽  
Usha Lamichhane ◽  
Mercedes Romero-Ruiz ◽  
Stephan Nussberger ◽  
Mathias Winterhalter
Keyword(s):  
Single Molecule ◽  
Temperature Dependent ◽  
Single Molecule Level ◽  
Channel Temperature

Atomic Force Microscopy (AFM) for Topography and Recognition Imaging at Single Molecule Level

2013 ◽  
pp. 102-112
Author(s):  
Memed Duman ◽  
Andreas Ebner ◽  
Christian Rankl ◽  
Jilin Tang ◽  
Lilia A. Chtcheglova ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Imaging

Curaxin-Induced DNA Topology Alterations Trigger the Distinct Binding Response of CTCF and FACT at the Single-Molecule Level

Biochemistry ◽  
2021 ◽  
Vol 60 (7) ◽  
pp. 494-499
Author(s):  
Ke Lu ◽  
Cuifang Liu ◽  
Yinuo Liu ◽  
Anfeng Luo ◽  
Jun Chen ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Topology ◽  
Single Molecule Level

scholarly journals Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model

2021 ◽  
Author(s):  
David A Garcia ◽  
Gregory Fettweis ◽  
Diego M Presman ◽  
Ville Paakinaho ◽  
Christopher Jarzynski ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Power Law ◽  
Dwell Time ◽  
Specific Binding ◽  
Power Law Distribution ◽  
Single Molecule Level ◽  
Binding Behavior ◽  
Chromatin Template ◽  
Nuclear Domains

Abstract Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs—one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.

Magnetic Nanoparticles as a Tool for Remote DNA Manipulations at a Single-Molecule Level

2021 ◽  
Vol 13 (12) ◽  
pp. 14458-14469
Author(s):  
Aleksey A. Nikitin ◽  
Anton Yu Yurenya ◽  
Timofei S. Zatsepin ◽  
Ilya O. Aparin ◽  
Vladimir P. Chekhonin ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Single Molecule ◽  
Single Molecule Level

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.

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