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Single-Molecule: From Physics to Biology
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Single-Molecule: From Physics to Biology

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 17382

Special Issue Editor

Dr. Francesco Simone Ruggeri

E-Mail Website
Guest Editor
Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge CB2 1EW, UK
Interests: single-molecule biophysics; nanoscale spectroscopy; atomic force microscopy; molecular biology; neurodegeneration

Special Issue Information

Dear Colleagues,

Biological processes rely on a wide class of biomolecular and macromolecular machines that have characteristic nanoscale physical dimensions and whose function emerges from their morphological, nanomechanical, chemical, and structural properties. A fundamental objective of modern biophysics is to progress the comprehension of the fundamental biomolecular processes underlying life and disease by studying the biophysical properties of biomolecules at the single-molecule scale.

To address this challenge, several imaging techniques working beyond the optical diffraction limit have been developed to visualize and investigate the biophysical properties of biological samples at the nanoscale, such as single-molecule fluorescence, scanning probe microscopy, nanoscale spectroscopy, and electron microscopy.

This Special Issue on “Single Molecule: from Physics to Biology” calls for manuscripts developing and/or applying physical methods in biology to unravel properties of biomolecules and biomolecular processes in cell function, human health, and disease.

Dr. Francesco Simone Ruggeri
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • single-molecule biophysics
  • microscopy
  • nanoscale spectroscopy
  • atomic force microscopy
  • electron microscopy
  • fluorescence
  • molecular and structural biology

Published Papers (5 papers)

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Research

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12 pages, 3019 KiB  
Article
A Horizontal Magnetic Tweezers for Studying Single DNA Molecules and DNA-Binding Proteins
by Roberto Fabian, Jr., Santosh Gaire, Christopher Tyson, Raghabendra Adhikari, Ian Pegg and Abhijit Sarkar
Molecules 2021, 26(16), 4781; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26164781 - 07 Aug 2021
Cited by 7 | Viewed by 3046
Abstract
We report data from single molecule studies on the interaction between single DNA molecules and core histones using custom-designed horizontal magnetic tweezers. The DNA-core histone complexes were formed using λ-DNA tethers, core histones, and NAP1 and were exposed to forces ranging from ~2 [...] Read more.
We report data from single molecule studies on the interaction between single DNA molecules and core histones using custom-designed horizontal magnetic tweezers. The DNA-core histone complexes were formed using λ-DNA tethers, core histones, and NAP1 and were exposed to forces ranging from ~2 pN to ~74 pN. During the assembly events, we observed the length of the DNA decrease in approximate integer multiples of ~50 nm, suggesting the binding of the histone octamers to the DNA tether. During the mechanically induced disassembly events, we observed disruption lengths in approximate integer multiples of ~50 nm, suggesting the unbinding of one or more octamers from the DNA tether. We also observed histone octamer unbinding events at forces as low as ~2 pN. Our horizontal magnetic tweezers yielded high-resolution, low-noise data on force-mediated DNA-core histone assembly and disassembly processes. Full article
(This article belongs to the Special Issue Single-Molecule: From Physics to Biology)
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12 pages, 2412 KiB  
Article
Infrared Nanospectroscopy of Individual Extracellular Microvesicles
by Raffaella Polito, Mattia Musto, Maria Eleonora Temperini, Laura Ballerini, Michele Ortolani, Leonetta Baldassarre, Loredana Casalis and Valeria Giliberti
Molecules 2021, 26(4), 887; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26040887 - 08 Feb 2021
Cited by 7 | Viewed by 2564
Abstract
Extracellular vesicles are membrane-delimited structures, involved in several inter-cellular communication processes, both physiological and pathological, since they deliver complex biological cargo. Extracellular vesicles have been identified as possible biomarkers of several pathological diseases; thus, their characterization is fundamental in order to gain a [...] Read more.
Extracellular vesicles are membrane-delimited structures, involved in several inter-cellular communication processes, both physiological and pathological, since they deliver complex biological cargo. Extracellular vesicles have been identified as possible biomarkers of several pathological diseases; thus, their characterization is fundamental in order to gain a deep understanding of their function and of the related processes. Traditional approaches for the characterization of the molecular content of the vesicles require a large quantity of sample, thereby providing an average molecular profile, while their heterogeneity is typically probed by non-optical microscopies that, however, lack the chemical sensitivity to provide information of the molecular cargo. Here, we perform a study of individual microvesicles, a subclass of extracellular vesicles generated by the outward budding of the plasma membrane, released by two cultures of glial cells under different stimuli, by applying a state-of-the-art infrared nanospectroscopy technique based on the coupling of an atomic force microscope and a pulsed laser, which combines the label-free chemical sensitivity of infrared spectroscopy with the nanometric resolution of atomic force microscopy. By correlating topographic, mechanical and spectroscopic information of individual microvesicles, we identified two main populations in both families of vesicles released by the two cell cultures. Subtle differences in terms of nucleic acid content among the two families of vesicles have been found by performing a fitting procedure of the main nucleic acid vibrational peaks in the 1000–1250 cm−1 frequency range. Full article
(This article belongs to the Special Issue Single-Molecule: From Physics to Biology)
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21 pages, 2663 KiB  
Article
An Estimation Algorithm for General Linear Single Particle Tracking Models with Time-Varying Parameters
by Boris I. Godoy, Nicholas A. Vickers and Sean B. Andersson
Molecules 2021, 26(4), 886; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26040886 - 08 Feb 2021
Cited by 7 | Viewed by 2535
Abstract
Single Particle Tracking (SPT) is a powerful class of methods for studying the dynamics of biomolecules inside living cells. The techniques reveal the trajectories of individual particles, with a resolution well below the diffraction limit of light, and from them the parameters defining [...] Read more.
Single Particle Tracking (SPT) is a powerful class of methods for studying the dynamics of biomolecules inside living cells. The techniques reveal the trajectories of individual particles, with a resolution well below the diffraction limit of light, and from them the parameters defining the motion model, such as diffusion coefficients and confinement lengths. Most existing algorithms assume these parameters are constant throughout an experiment. However, it has been demonstrated that they often vary with time as the tracked particles move through different regions in the cell or as conditions inside the cell change in response to stimuli. In this work, we propose an estimation algorithm to determine time-varying parameters of systems that discretely switch between different linear models of motion with Gaussian noise statistics, covering dynamics such as diffusion, directed motion, and Ornstein–Uhlenbeck dynamics. Our algorithm consists of three stages. In the first stage, we use a sliding window approach, combined with Expectation Maximization (EM) to determine maximum likelihood estimates of the parameters as a function of time. These results are only used to roughly estimate the number of model switches that occur in the data to guide the selection of algorithm parameters in the second stage. In the second stage, we use Change Detection (CD) techniques to identify where the models switch, taking advantage of the off-line nature of the analysis of SPT data to create non-causal algorithms with better precision than a purely causal approach. Finally, we apply EM to each set of data between the change points to determine final parameter estimates. We demonstrate our approach using experimental data generated in the lab under controlled conditions. Full article
(This article belongs to the Special Issue Single-Molecule: From Physics to Biology)
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Review

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28 pages, 33728 KiB  
Review
DNA Manipulation and Single-Molecule Imaging
by Shunsuke Takahashi, Masahiko Oshige and Shinji Katsura
Molecules 2021, 26(4), 1050; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26041050 - 17 Feb 2021
Cited by 3 | Viewed by 4812
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been [...] Read more.
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein. Full article
(This article belongs to the Special Issue Single-Molecule: From Physics to Biology)
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20 pages, 2533 KiB  
Review
Single Molecule Characterization of Amyloid Oligomers
by Jie Yang, Sarah Perrett and Si Wu
Molecules 2021, 26(4), 948; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26040948 - 11 Feb 2021
Cited by 10 | Viewed by 3704
Abstract
The misfolding and aggregation of polypeptide chains into β-sheet-rich amyloid fibrils is associated with a wide range of neurodegenerative diseases. Growing evidence indicates that the oligomeric intermediates populated in the early stages of amyloid formation rather than the mature fibrils are responsible for [...] Read more.
The misfolding and aggregation of polypeptide chains into β-sheet-rich amyloid fibrils is associated with a wide range of neurodegenerative diseases. Growing evidence indicates that the oligomeric intermediates populated in the early stages of amyloid formation rather than the mature fibrils are responsible for the cytotoxicity and pathology and are potentially therapeutic targets. However, due to the low-populated, transient, and heterogeneous nature of amyloid oligomers, they are hard to characterize by conventional bulk methods. The development of single molecule approaches provides a powerful toolkit for investigating these oligomeric intermediates as well as the complex process of amyloid aggregation at molecular resolution. In this review, we present an overview of recent progress in characterizing the oligomerization of amyloid proteins by single molecule fluorescence techniques, including single-molecule Förster resonance energy transfer (smFRET), fluorescence correlation spectroscopy (FCS), single-molecule photobleaching and super-resolution optical imaging. We discuss how these techniques have been applied to investigate the different aspects of amyloid oligomers and facilitate understanding of the mechanism of amyloid aggregation. Full article
(This article belongs to the Special Issue Single-Molecule: From Physics to Biology)
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