scholarly journals Single molecule studies of DNA bending, looping and compacting proteins using optical tweezers and atomic force microscopy

2017 ◽  
Author(s):  
Murugesapillai
Keyword(s):  
Atomic Force Microscopy ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Dna Bending ◽  
Force Microscopy ◽  
Atomic Force ◽  
Single Molecule Studies

Revisiting atomic force microscopy force spectroscopy sensitivity for single molecule studies

2008 ◽  
Vol 104 (11) ◽  
pp. 114504 ◽  
Author(s):  
Shahid Naeem ◽  
Yu Liu ◽  
Heng-Yong Nie ◽  
W. M. Lau ◽  
Jun Yang
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Force Microscopy ◽  
Atomic Force ◽  
Single Molecule Studies

scholarly journals Watching biological nanomotors at work : insights from single-molecule studies

2017 ◽  
Author(s):  
◽  
Nagaraju Chada
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Halobacterium Salinarum ◽  
Biological Processes ◽  
Enzyme Dynamics ◽  
Oligomeric State ◽  
Force Microscopy ◽  
Atomic Force ◽  
Single Molecule Studies

Recent decades have seen several complimentary biophysics tools emerge to study single protein macromolecules. Most of these techniques use glass as a specimen support. The atomic force microscope, a vital tool in biophysics suited to study proteins in their near native environments, uses mica as a specimen support, as it is known for its extreme flatness and ease of use. Here we optimized glass as a specimen support for atomic force microscopy. This enables the combination of other single molecule techniques with atomic force microscopy to study the same protein macromolecular system in unison. Using bacteriorhodopsin from Halobacterium salinarum and the Sec-translocase (SecA/SecYEG) from Escherichia coli, we demonstrate that faithful images of 2D crystalline and non-crystalline membrane proteins in lipid bilayers can be obtained on common microscope cover glass following a straight-forward cleaning procedure. Repeated association and dissociation of SecA with SecYEG indicated that the proteins remain competent for biological processes on glass supports for long periods of time. This work opens the door for combining high resolution biological AFM with other powerful complementary single molecule techniques that require glass as a specimen support. In the second part of this work we studied SecA-ATP hydrolysis and catalase enzyme dynamics. Both of these protein macromolecules were observed to be highly dynamic during catalytic turnover. Single molecule studies of catalase indicated that the enzyme undergoes significant dynamics including oligomeric state changes when exposed to H2O2. Conformational dynamics of the SecA-ATPase was visualized at the single molecule level and the protein macromolecule was observed to flicker between a compact and expanded state in the presence of ATP, indicating reversible conformational changes. Future studies in the lab will shed more light onto these important biological processes.

scholarly journals Bioconjugation Strategies for Connecting Proteins to DNA-Linkers for Single-Molecule Force-Based Experiments

Nanomaterials ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2424
Author(s):  
Lyan M. van der Sleen ◽  
Katarzyna M. Tych
Keyword(s):  
Mechanical Properties ◽  
Atomic Force Microscopy ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Short Range ◽  
Force Spectroscopy ◽  
Magnetic Tweezers ◽  
Single Molecule Force Spectroscopy ◽  
Force Microscopy ◽  
Atomic Force

The mechanical properties of proteins can be studied with single molecule force spectroscopy (SMFS) using optical tweezers, atomic force microscopy and magnetic tweezers. It is common to utilize a flexible linker between the protein and trapped probe to exclude short-range interactions in SMFS experiments. One of the most prevalent linkers is DNA due to its well-defined properties, although attachment strategies between the DNA linker and protein or probe may vary. We will therefore provide a general overview of the currently existing non-covalent and covalent bioconjugation strategies to site-specifically conjugate DNA-linkers to the protein of interest. In the search for a standardized conjugation strategy, considerations include their mechanical properties in the context of SMFS, feasibility of site-directed labeling, labeling efficiency, and costs.

Single-molecule studies of DNA transcription using atomic force microscopy

2012 ◽  
Vol 9 (2) ◽  
pp. 021001 ◽  
Author(s):  
Daniel J Billingsley ◽  
William A Bonass ◽  
Neal Crampton ◽  
Jennifer Kirkham ◽  
Neil H Thomson
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Dna Transcription ◽  
Force Microscopy ◽  
Atomic Force ◽  
Single Molecule Studies

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

scholarly journals Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 687
Author(s):  
Amna Abdalla Mohammed Khalid ◽  
Pietro Parisse ◽  
Barbara Medagli ◽  
Silvia Onesti ◽  
Loredana Casalis
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Complex ◽  
The Other ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mcm Complex ◽  
Dna Double Helix

The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.

Substrate Specificity of Sugar Transport by Rabbit SGLT1:  Single-Molecule Atomic Force Microscopy versus Transport Studies†

Biochemistry ◽  
2007 ◽  
Vol 46 (10) ◽  
pp. 2797-2804 ◽  
Author(s):  
Theeraporn Puntheeranurak ◽  
Barbara Wimmer ◽  
Francisco Castaneda ◽  
Hermann J. Gruber ◽  
Peter Hinterdorfer ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Substrate Specificity ◽  
Single Molecule ◽  
Sugar Transport ◽  
Force Microscopy ◽  
Atomic Force ◽  
Transport Studies

Breaking Down the Supramolecular Ensemble: Single-Molecule Studies of the Concentration Dependence of Main-Chain Supramolecular Polymer Molecular Weight Distributions on Surfaces

2010 ◽  
Vol 63 (4) ◽  
pp. 624
Author(s):  
Michael J. Serpe ◽  
Jason R. Whitehead ◽  
Stephen L. Craig
Keyword(s):  
Molecular Weight ◽  
Single Molecule ◽  
Monomer Concentration ◽  
Supramolecular Polymer ◽  
Force Microscopy ◽  
Molecular Weight Distributions ◽  
Atomic Force ◽  
Multi Stage ◽  
Single Molecule Studies ◽  
Supramolecular Ensemble

Single molecule atomic force microscopy (AFM) studies of oligonucleotide-based supramolecular polymers on surfaces are used to examine the molecular weight distribution of the polymers formed between a functionalized surface and an AFM tip as a function of monomer concentration. For the concentrations examined here, excellent agreement with a multi-stage open association model of polymerization is obtained, without the need to invoke additional contributions from secondary steric interactions at the surface.

Sign in / Sign up

Export Citation Format

Share Document