Micro Technologies for Single Molecule Manipulation and Detection

A special issue of Micromachines (ISSN 2072-666X). This special issue belongs to the section "B:Biology and Biomedicine".

Deadline for manuscript submissions: closed (31 July 2018) | Viewed by 15781

Special Issue Editor

Departments of Mechanical Engineering, Biomedical Engineering and Oncology, Johns Hopkins University, 108 Latrobe, 3400 N. Charles Street, Baltimore, MD 21218, USA
Interests: new technologies and methods for molecular analysis of diseases and biomedical research; nano-biosensors; single-molecule fluorescence spectroscopy; microfluidics; genetic and epigenetic biomarker detection of cancer and infectious diseases
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Special Issue Information

Dear Colleagues,

Single molecule studies facilitate our understanding of the fundamental molecular process in the biological system. Measurements of biomolecules at the single molecule resolution help explore biological riddles and reveal heterogeneities hidden in the ensembles. Microtechnologies such as microfluidics and microfabrication technologies play several roles in this particular form of analysis and measurements. Detection of single molecules requires decreasing the background noise below the signal emitted by each molecule by limiting the source of noises. This can be achieved by decreasing the volume of interrogation by confinement of molecules in micro- or nano-scale configurations. The small-scale devices can also be designed to complement high sensitivity single molecule detectors by enhancing the signal emitted from each molecule. Alternatively, compartmentalization of signal amplification reactions to small micro-reactors such as droplets or wells can be used to increase the local concentration of single-emitted molecules. This Special Issue seeks to feature research papers, short communications, and review articles that focus on novel technological developments of manipulation and detection of single biomolecules such as DNA, RNA and proteins.

Prof. Jeff Tza-Huei Wang
Guest Editor

Manuscript Submission Information

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Keywords

  • Single molecule detection

  • Single molecule manipulation

  • Microfluidics

  • Microfabrication

  • Molecular confinement/stretching

Published Papers (3 papers)

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Research

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12 pages, 5116 KiB  
Article
A Horizontal Magnetic Tweezers and Its Use for Studying Single DNA Molecules
by Roberto Fabian, Jr., Christopher Tyson, Pamela L. Tuma, Ian Pegg and Abhijit Sarkar
Micromachines 2018, 9(4), 188; https://doi.org/10.3390/mi9040188 - 17 Apr 2018
Cited by 12 | Viewed by 5273
Abstract
We report the development of a magnetic tweezers that can be used to micromanipulate single DNA molecules by applying picoNewton (pN)-scale forces in the horizontal plane. The resulting force–extension data from our experiments show high-resolution detection of changes in the DNA tether’s extension: [...] Read more.
We report the development of a magnetic tweezers that can be used to micromanipulate single DNA molecules by applying picoNewton (pN)-scale forces in the horizontal plane. The resulting force–extension data from our experiments show high-resolution detection of changes in the DNA tether’s extension: ~0.5 pN in the force and <10 nm change in extension. We calibrate our instrument using multiple orthogonal techniques including the well-characterized DNA overstretching transition. We also quantify the repeatability of force and extension measurements, and present data on the behavior of the overstretching transition under varying salt conditions. The design and experimental protocols are described in detail, which should enable straightforward reproduction of the tweezers. Full article
(This article belongs to the Special Issue Micro Technologies for Single Molecule Manipulation and Detection)
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Review

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15 pages, 2753 KiB  
Review
Friction Determination by Atomic Force Microscopy in Field of Biochemical Science
by Yan Wang and Jianhua Wang
Micromachines 2018, 9(7), 313; https://doi.org/10.3390/mi9070313 - 21 Jun 2018
Cited by 15 | Viewed by 5146
Abstract
Atomic force microscopy (AFM) is an analytical nanotechnology in friction determination between microscale and nanoscale surfaces. AFM has advantages in mechanical measurement, including high sensitivity, resolution, accuracy, and simplicity of operation. This paper will introduce the principles of mechanical measurement by using AFM [...] Read more.
Atomic force microscopy (AFM) is an analytical nanotechnology in friction determination between microscale and nanoscale surfaces. AFM has advantages in mechanical measurement, including high sensitivity, resolution, accuracy, and simplicity of operation. This paper will introduce the principles of mechanical measurement by using AFM and reviewing the progress of AFM methods in determining frictions in the field of biochemical science over the past decade. While three friction measurement assays—friction morphology, friction curve and friction process in experimental cases—are mainly introduced, important advances of technology, facilitating future development of AFM are also discussed. In addition to the principles and advances, the authors also give an overview of the shortcomings and restrictions of current AFM methods, and propose potential directions of AFM techniques by combining it with other well-established characterization techniques. AFM methods are expected to see an increase in development and attract wide attention in scientific research. Full article
(This article belongs to the Special Issue Micro Technologies for Single Molecule Manipulation and Detection)
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23 pages, 2506 KiB  
Review
Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination
by Hsiu-Fang Fan, Chien-Hui Ma and Makkuni Jayaram
Micromachines 2018, 9(5), 216; https://doi.org/10.3390/mi9050216 - 03 May 2018
Cited by 9 | Viewed by 4998
Abstract
Tethered particle motion/microscopy (TPM) is a biophysical tool used to analyze changes in the effective length of a polymer, tethered at one end, under changing conditions. The tether length is measured indirectly by recording the Brownian motion amplitude of a bead attached to [...] Read more.
Tethered particle motion/microscopy (TPM) is a biophysical tool used to analyze changes in the effective length of a polymer, tethered at one end, under changing conditions. The tether length is measured indirectly by recording the Brownian motion amplitude of a bead attached to the other end. In the biological realm, DNA, whose interactions with proteins are often accompanied by apparent or real changes in length, has almost exclusively been the subject of TPM studies. TPM has been employed to study DNA bending, looping and wrapping, DNA compaction, high-order DNA–protein assembly, and protein translocation along DNA. Our TPM analyses have focused on tyrosine and serine site-specific recombinases. Their pre-chemical interactions with DNA cause reversible changes in DNA length, detectable by TPM. The chemical steps of recombination, depending on the substrate and the type of recombinase, may result in a permanent length change. Single molecule TPM time traces provide thermodynamic and kinetic information on each step of the recombination pathway. They reveal how mechanistically related recombinases may differ in their early commitment to recombination, reversibility of individual steps, and in the rate-limiting step of the reaction. They shed light on the pre-chemical roles of catalytic residues, and on the mechanisms by which accessory proteins regulate recombination directionality. Full article
(This article belongs to the Special Issue Micro Technologies for Single Molecule Manipulation and Detection)
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