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DNA-Based Sensors for Single-Molecule Biology
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DNA-Based Sensors for Single-Molecule Biology

A special issue of Sensors (ISSN 1424-8220). This special issue belongs to the section "Biosensors".

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 30059

Special Issue Editors

Prof. Dr. Isaac Li

E-Mail Website
Guest Editor
Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada
Interests: single-molecule force spectroscopy; single-molecule fluorescence; DNA-based biosensors and molecular devices; mechanobiology; molecular force sensors
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yong Wang

E-Mail Website
Guest Editor
Department of Physics, University of Arkansas, Fayetteville, Arkansas, USA
Interests: single-molecule fluorescence, DNA-based biosensors and devices, mechanics and dynamics of biological systems, antimicrobial mechanisms of metal nano-structures

Special Issue Information

Dear colleagues,

This special issue of Sensors will be dedicated to DNA-based molecular sensors for studying biological processes at the single-molecule level. Molecular biosensors have played a crucial role in understanding biological systems from the single-cell level to tissues and organisms. The detection of individual, single-molecule events in a single cell is necessary to gain insight into the heterogeneity, spatial distribution, noise, sensitivity, and regulation of molecular processes in the cells. Research into DNA-based molecular sensors has been exceptionally active, as a result of their “programmable” nature, in the creation of designer structural (e.g., DNA origami), function (e.g., DNAzymes), and detection/imaging (e.g., DNA-PAINT) elements.

In this special issue, we will feature the most recent progress in this field, from modelling and simulation studies to the development of new constructs of DNA-based sensors, as well as new experimental methods using these sensors for imaging and detection.

Potential topics include but are not limited to the following:

  • Cellular processes sensing (e.g., metabolite, tension, signalling);
  • DNA origami and supramolecular assembly;
  • Single-molecule and super-resolution imaging;
  • Single-molecule force spectroscopy;
  • Imaging technique and method development;
  • Modelling and simulation;
  • Theoretical sensing strategy.
Prof. Dr. Isaac Li
Prof. Dr. Yong Wang
Guest Editors

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. Sensors 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 2600 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

  • DNA/RNA/Nucleic acid
  • Single-molecule
  • Imaging
  • Force spectroscopy
  • Biosensor
  • Super-resolution
  • Molecular structures.

Published Papers (6 papers)

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Research

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10 pages, 1905 KiB  
Article
Aptamer-Conjugated Polydiacetylene Colorimetric Paper Chip for the Detection of Bacillus thuringiensis Spores
by Chaoge Zhou, Taeyeong You, Huisoo Jang, Hyunil Ryu, Eun-Seon Lee, Mi-Hwa Oh, Yun Suk Huh, Sun Min Kim and Tae-Joon Jeon
Sensors 2020, 20(11), 3124; https://doi.org/10.3390/s20113124 - 01 Jun 2020
Cited by 19 | Viewed by 4182
Abstract
A colorimetric polydiacetylene (PDA) paper strip sensor that can specifically recognize Bacillus thuringiensis (BT) HD-73 spores is described in this work. The target-specific aptamer was combined with PDA, and the aptamer-conjugated PDA vesicles were then coated on polyvinylidene fluoride (PVDF) paper strips by [...] Read more.
A colorimetric polydiacetylene (PDA) paper strip sensor that can specifically recognize Bacillus thuringiensis (BT) HD-73 spores is described in this work. The target-specific aptamer was combined with PDA, and the aptamer-conjugated PDA vesicles were then coated on polyvinylidene fluoride (PVDF) paper strips by a simple solvent evaporation method. The PDA-aptamer paper strips can be used to detect the target without any pre-treatment. Using the paper strip, the presence of BT spores is directly observable by the naked eye based on the unique blue-to-red color transition of the PDA. Quantitative studies using the paper strip were also carried out by analyzing the color transitions of the PDA. The specificity of this PDA sensor was verified with a high concentration of Escherichia coli, and no discernable change was observed. The observable color change in the paper strip occurs in less than 1 h, and the limit of detection is 3 × 107 CFU/mL, much below the level harmful to humans. The PDA-based paper sensor, developed in this work, does not require a separate power or detection device, making the sensor strip highly transportable and suitable for spore analysis anytime and anywhere. Moreover, this paper sensor platform is easily fabricated, can be adapted to other targets, is highly portable, and is highly specific for the detection of BT spores. Full article
(This article belongs to the Special Issue DNA-Based Sensors for Single-Molecule Biology)
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17 pages, 3114 KiB  
Article
Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules
by Jack Freeland, Lihua Zhang, Shih-Ting Wang, Mason Ruiz and Yong Wang
Sensors 2020, 20(11), 3112; https://doi.org/10.3390/s20113112 - 31 May 2020
Cited by 2 | Viewed by 3558
Abstract
Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to [...] Read more.
Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs. Full article
(This article belongs to the Special Issue DNA-Based Sensors for Single-Molecule Biology)
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Review

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18 pages, 5887 KiB  
Review
Genetically Encoded Biosensors Based on Fluorescent Proteins
by Hyunbin Kim, Jeongmin Ju, Hae Nim Lee, Hyeyeon Chun and Jihye Seong
Sensors 2021, 21(3), 795; https://doi.org/10.3390/s21030795 - 25 Jan 2021
Cited by 26 | Viewed by 9017
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) allow for the real-time monitoring of molecular dynamics in space and time, which are crucial for the proper functioning and regulation of complex cellular processes. Depending on the types of molecular events to be monitored, [...] Read more.
Genetically encoded biosensors based on fluorescent proteins (FPs) allow for the real-time monitoring of molecular dynamics in space and time, which are crucial for the proper functioning and regulation of complex cellular processes. Depending on the types of molecular events to be monitored, different sensing strategies need to be applied for the best design of FP-based biosensors. Here, we review genetically encoded biosensors based on FPs with various sensing strategies, for example, translocation, fluorescence resonance energy transfer (FRET), reconstitution of split FP, pH sensitivity, maturation speed, and so on. We introduce general principles of each sensing strategy and discuss critical factors to be considered if available, then provide representative examples of these FP-based biosensors. These will help in designing the best sensing strategy for the successful development of new genetically encoded biosensors based on FPs. Full article
(This article belongs to the Special Issue DNA-Based Sensors for Single-Molecule Biology)
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14 pages, 1920 KiB  
Review
Recent Advances in Cell Adhesive Force Microscopy
by Ying Tu and Xuefeng Wang
Sensors 2020, 20(24), 7128; https://doi.org/10.3390/s20247128 - 12 Dec 2020
Cited by 6 | Viewed by 3845
Abstract
Cell adhesive force, exerting on the local matrix or neighboring cells, plays a critical role in regulating many cell functions and physiological processes. In the past four decades, significant efforts have been dedicated to cell adhesive force detection, visualization and quantification. A recent [...] Read more.
Cell adhesive force, exerting on the local matrix or neighboring cells, plays a critical role in regulating many cell functions and physiological processes. In the past four decades, significant efforts have been dedicated to cell adhesive force detection, visualization and quantification. A recent important methodological advancement in cell adhesive force visualization is to adopt force-to-fluorescence conversion instead of force-to-substrate strain conversion, thus greatly improving the sensitivity and resolution of force imaging. This review summarizes the recent development of force imaging techniques (collectively termed as cell adhesive force microscopy or CAFM here), with a particular focus on the improvement of CAFM’s spatial resolution and the biomaterial choices for constructing the tension sensors used in force visualization. This review also highlights the importance of DNA-based tension sensors in cell adhesive force imaging and the recent breakthrough in the development of super-resolution CAFM. Full article
(This article belongs to the Special Issue DNA-Based Sensors for Single-Molecule Biology)
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24 pages, 3601 KiB  
Review
Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology
by Runjhun Saran, Yong Wang and Isaac T. S. Li
Sensors 2020, 20(24), 7019; https://doi.org/10.3390/s20247019 - 08 Dec 2020
Cited by 20 | Viewed by 6178
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical [...] Read more.
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA’s bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA’s rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines. Full article
(This article belongs to the Special Issue DNA-Based Sensors for Single-Molecule Biology)
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15 pages, 5335 KiB  
Review
Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy
by Seungah Lee, Indra Batjikh and Seong Ho Kang
Sensors 2020, 20(22), 6667; https://doi.org/10.3390/s20226667 - 21 Nov 2020
Cited by 3 | Viewed by 2706
Abstract
The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development [...] Read more.
The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development of SR microscopy methods, DNA nanostructures can now be optically assessed. Using the specific binding of fluorophores with their target molecules, advanced single-molecule localization microscopy (SMLM) has been expanded into different fields, allowing wide-range detection at the single-molecule level. This review discusses the recent progress in the SR imaging of DNA nano-objects using SMLM techniques, such as direct stochastic optical reconstruction microscopy, binding-activated localization microscopy, and point accumulation for imaging nanoscale topography. Furthermore, we discuss their advantages and limitations, present applications, and future perspectives. Full article
(This article belongs to the Special Issue DNA-Based Sensors for Single-Molecule Biology)
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