Photonics in Single Molecule Detection and Analysis Techniques

A special issue of Photonics (ISSN 2304-6732).

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 2810

Special Issue Editor

Department of Science and High Technology, Università degli Studi dell’Insubria, Via Valleggio, 11-22100 Como (CO), Italy
Interests: advanced fluorescence spectroscopy techniques; molecular biophysics; spectroscopic evaluation and optimization of drugs and drug delivery systems; photosensitizers; amyloid aggregation; new materials; polymeric metal-organic compounds
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Special Issue Information

Dear Colleagues,

In my personal research experience, I have had several clues that the lack of communication between the very wide and diverse actors of the “end-user” community raising the problems to be solved by means of single-molecule studies (spanning from molecular biologists to quantum physicists), and the scientists of the physical and engineering proficiencies which might provide them with the tools to find the pertaining solutions in the next future, is a major obstacle to the diffusion and optimal exploitation of single molecule techniques. Accordingly, this Special Issue of Photonics, devoted to techniques allowing the observation and analysis of molecular systems on a few-single molecule scale, does not have the ambition to constitute an exhaustive panorama of the state of art in this fascinating branch of physics; it is rather intended to provide an interdisciplinary forum for different professionals involved in the research on the topic. In particular, the ideal goal would be to present a number of challenging scientific topics requiring particularly demanding performances of experimental setups, identify the figures of merit required to optimally address such topics and involve technology experts to offer a comprehensive overview of the most innovative detectors and laser sources, both commercial and “out of market”, as well as scientists committed to devising or implementing strategies and methods to overcome the actual limits of single-molecule analysis in terms of intensity, spatial and temporal resolution.

This crosstalk should, in turn, provide a glancing view on the several interconnected aspects that are to be tackled in the next future, in the hope to offer a less sectorial point of view and, possibly, an occasion to develop new networks. To this aim, high quality original research articles are welcomed in the following and other related topics: single-molecule fluorescence resonance energy transfer and fluorescence fluctuation spectroscopy experiments; super-resolution fluorescence microscopy studies; manipulation and imaging techniques exploiting the ability of inducing or at least monitoring through photonics the response of single molecules to nano-mechanical stress, such as molecular tweezers and atomic force microscopy. Well documented reviews on either single-molecule techniques or the performances of detectors and light sources in single-molecule applications are also solicited.

Dr. Luca Nardo
Guest Editor

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Keywords

  • light sources and detectors for single-molecules photonics applications
  • single-molecule FRET
  • optical tweezers
  • atomic force microscopy
  • magnetic tweezers
  • fluorescence fluctuation spectroscopy
  • super-resolution microscopy

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Published Papers (2 papers)

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Review

18 pages, 2620 KiB  
Review
Probing G-Quadruplexes Conformational Dynamics and Nano-Mechanical Interactions at the Single Molecule Level: Techniques and Perspectives
by Marco Lamperti, Riccardo Rigo, Claudia Sissi and Luca Nardo
Photonics 2024, 11(11), 1061; https://doi.org/10.3390/photonics11111061 - 13 Nov 2024
Viewed by 567
Abstract
The analysis of nucleic acid structures, topologies, nano-mechanics and interactions with ligands and other biomacromolecules (most notably proteins) at the single molecule level has become a fundamental topic in molecular biophysics over the last two decades. Techniques such as molecular tweezers, single-molecule fluorescence [...] Read more.
The analysis of nucleic acid structures, topologies, nano-mechanics and interactions with ligands and other biomacromolecules (most notably proteins) at the single molecule level has become a fundamental topic in molecular biophysics over the last two decades. Techniques such as molecular tweezers, single-molecule fluorescence resonance energy transfer, and atomic force microscopy have enabled us to disclose an unprecedented insight into the mechanisms governing gene replication, transcription and regulation. In this minireview, we survey the main working principles and discuss technical caveats of the above techniques, using as a fil-rouge the history of their achievements in dissecting G-quadruplexes. The revised literature offers a clear example of the superior ability of single-molecule techniques with respect to ensemble techniques to unveil the structural and functional diversity of the several polymorphs corresponding to a single G-quadruplex folding sequence, thus shedding new light on the extreme complexity of these fascinating non-Watson–Crick structures. Full article
(This article belongs to the Special Issue Photonics in Single Molecule Detection and Analysis Techniques)
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36 pages, 21309 KiB  
Review
Conformational Dynamics of Biopolymers in the Course of Their Interaction: Multifaceted Approaches to the Analysis by the Stopped-Flow Technique with Fluorescence Detection
by Nikita A. Kuznetsov
Photonics 2023, 10(9), 1033; https://doi.org/10.3390/photonics10091033 - 8 Sep 2023
Cited by 2 | Viewed by 1348
Abstract
This review deals with modern approaches to systematic research on molecular-kinetic mechanisms of damage recognition and removal by pro- and eukaryotic enzymes of DNA base excision repair. To this end, using DNA glycosylases from different structural families as an example—as well as apurinic/apyrimidinic [...] Read more.
This review deals with modern approaches to systematic research on molecular-kinetic mechanisms of damage recognition and removal by pro- and eukaryotic enzymes of DNA base excision repair. To this end, using DNA glycosylases from different structural families as an example—as well as apurinic/apyrimidinic endonuclease, which differs structurally and catalytically from DNA glycosylases—a comprehensive methodology is described in detail regarding studies on the mechanisms of action of DNA repair enzymes in humans and in Escherichia coli. This methodology is based on kinetic, thermodynamic, and mutational analyses of alterations in the conformation of molecules of an enzyme and of DNA during their interaction in real time. The described techniques can be used to analyze any protein–protein or protein–nucleic acid interactions. Full article
(This article belongs to the Special Issue Photonics in Single Molecule Detection and Analysis Techniques)
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