Single-Molecule Sensing for Biomedical Applications

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 7851

Special Issue Editor

Institute of Science and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka 567-0047, Japan
Interests: single-molecule analysis; nanotechnology; quantum chemistry; artificial intelligence; analytical chemistry; biopolymer
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Special Issue Information

Dear Colleagues,

The development of single-molecule sensing is one of the challenges in the field of applied science. Until now, single-molecule sensing has been used in basic research for the study of various physical phenomena, chemical reactions, and elemental biological processes. The recent rapid development of nanotechnology enables the reproducible fabrication and integration of molecular-size functional nanospacers, such as nanopores, nanogaps, nanochannels, nanoparticles. Therefore, single-molecule sensing technology has become available for various biomedical application.

In the field of medical application research, a personal medical care system, called “precision medicine”, has been recently attracting attention. In this field, sensors can allow the simultaneous detection and quantitative analysis of various kinds of biomolecules such as DNA and RNA, proteins, their epi-modifications, as well as other biomarkers and even very rare biomolecules required for disease diagnosis. Moreover, biocompatible and wearable sensors are also useful for non-invasive monitoring and pretreatment technology for biosampling, such as liquid biopsies. 

Therefore, single-molecule sensing is an ideal medical technique for the realization of precision-medicine systems. This is because it allows accurate judgment and diagnoses by measuring various biomarker molecules at the same time. In addition, the integration of pretreatment in single-molecule sensing devices is important for the production of non-invasive, biocompatible, and wearable sensors. 

This Special Issue will focus on single-molecule sensing for biomedical applications, including electrical, optical, and/or magnetic measurements and nano/micro fabrication technologies for devices using nanostructures such as nanopores, nanogaps, nanochannels, MEMS, NEMS, etc. It will also welcome pretreatment studies for biomedical sensing, aimed at the development of sensors for single-molecule detection, integrating purification, extraction, molecular control, as well as for non-invasive, biocompatible, and wearable functional devices. In addition, for single-molecule analysis, studies on artificial intelligence, such as multivariate analysis, machine learning, and deep learning, and molecular simulation methods are also of interest.

Prof. Takahito Ohshiro
Guest Editor

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Keywords

  • Single-molecule detection/identification methods for biomedical application such as personal medicine, precision medicine
  • Single-molecule detection methods using electrical, optical, and magnetic measurements including microscopy, and probe technique
  • Single-molecule analysis methodology using artificial intelligence and molecular simulation
  • Devices Integrating MEMS, NEMS, and channel for sensing, and pretreatment for non-invasive, biocompatible and wearable sensors

Published Papers (4 papers)

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Research

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9 pages, 2762 KiB  
Article
Theoretical Computational Analysis Predicts Interaction Changes Due to Differences of a Single Molecule in DNA
by Jun Koseki, Haruka Hirose, Masamitsu Konno and Teppei Shimamura
Appl. Sci. 2023, 13(1), 510; https://0-doi-org.brum.beds.ac.uk/10.3390/app13010510 - 30 Dec 2022
Cited by 1 | Viewed by 1001
Abstract
Theoretical methods, such as molecular mechanics and molecular dynamics, are very useful in understanding differences in interactions at the single molecule level. In the life sciences, small conformational changes, including substituent modifications, often have a significant impact on function in vivo. Changes in [...] Read more.
Theoretical methods, such as molecular mechanics and molecular dynamics, are very useful in understanding differences in interactions at the single molecule level. In the life sciences, small conformational changes, including substituent modifications, often have a significant impact on function in vivo. Changes in binding interactions between nucleic acid molecules and binding proteins are a prime example. In this study, we propose a strategy to predict the complex structure of DNA-binding proteins with arbitrary DNA and analyze the differences in their interactions. We tested the utility of our strategy using the anticancer drug trifluoro-thymidine (FTD), which exerts its pharmacological effect by incorporation into DNA, and confirmed that the binding affinity of the BCL-2-associated X sequence to the p53 tetramer is increased by FTD incorporation. On the contrary, in p53-binding sequences extracted from FTD-resistant cells, the binding affinity of DNA containing FTD was found to be greatly reduced compared to normal DNA. This suggests that thymidine randomly substituted for FTD in resistant cells may acquire resistance by entering a position that inhibits binding to DNA-binding proteins. We believe that this is a versatile procedure that can also take energetics into account and will increase the importance of computational science in the life sciences. Full article
(This article belongs to the Special Issue Single-Molecule Sensing for Biomedical Applications)
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9 pages, 1726 KiB  
Article
Quenching Efficiency of Quantum Dots Conjugated to Lipid Bilayers on Graphene Oxide Evaluated by Fluorescence Single Particle Tracking
by Yoshiaki Okamoto, Seiji Iwasa and Ryugo Tero
Appl. Sci. 2022, 12(8), 3733; https://0-doi-org.brum.beds.ac.uk/10.3390/app12083733 - 07 Apr 2022
Cited by 4 | Viewed by 1495
Abstract
A single particle observation of quantum dots (QDs) was performed on lipid bilayers formed on graphene oxide (GO). The long-range fluorescence quenching of GO has been applied to biosensing for various biomolecules. We demonstrated the single particle observation of a QD on supported [...] Read more.
A single particle observation of quantum dots (QDs) was performed on lipid bilayers formed on graphene oxide (GO). The long-range fluorescence quenching of GO has been applied to biosensing for various biomolecules. We demonstrated the single particle observation of a QD on supported lipid bilayers in this study, aiming to detect the quenching efficiency of lipid and protein molecules in a lipid bilayer by fluorescence single particle tacking (SPT). A single lipid bilayer or double lipid bilayers were formed on GO flakes deposited on a thermally oxidized silicon substrate by the vesicle fusion method. The QDs were conjugated on the lipid bilayers, and single particle images of the QDs were obtained under the quenching effect of GO. The quenching efficiency of a single QD was evaluated from the fluorescence intensities on the regions with and without GO. The quenching efficiency reflecting the layer numbers of the lipid bilayers was obtained. Full article
(This article belongs to the Special Issue Single-Molecule Sensing for Biomedical Applications)
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Review

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16 pages, 2341 KiB  
Review
RNA Modification Related Diseases and Sensing Methods
by Mayuka Ohkawa and Masamitsu Konno
Appl. Sci. 2023, 13(11), 6376; https://0-doi-org.brum.beds.ac.uk/10.3390/app13116376 - 23 May 2023
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Abstract
Epitranscriptomics is the study of RNA base modifications, including functionally relevant transcriptomic changes. Epitranscriptomics has been actively studied in recent years and has been reported to play important roles in development, homeostasis, the immune system, and various life phenomena such as cancer, neurological [...] Read more.
Epitranscriptomics is the study of RNA base modifications, including functionally relevant transcriptomic changes. Epitranscriptomics has been actively studied in recent years and has been reported to play important roles in development, homeostasis, the immune system, and various life phenomena such as cancer, neurological diseases, and infectious diseases. However, a major problem is the development of sequencing methods to map RNA base modifications throughout the transcriptome. In recent years, various methods for RNA base modification have been actively studied, and we are beginning to successfully measure base modifications that have been difficult to measure in previous years. In this review, we will discuss in detail the biological significance of RNA modifications and the latest techniques for detecting RNA modifications. Full article
(This article belongs to the Special Issue Single-Molecule Sensing for Biomedical Applications)
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20 pages, 900 KiB  
Review
Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method
by Takahito Ohshiro
Appl. Sci. 2022, 12(3), 1539; https://0-doi-org.brum.beds.ac.uk/10.3390/app12031539 - 31 Jan 2022
Cited by 6 | Viewed by 3125
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection [...] Read more.
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement. Full article
(This article belongs to the Special Issue Single-Molecule Sensing for Biomedical Applications)
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