Next Article in Journal
CO2 Laser-Based Rapid Prototyping of Micropumps
Next Article in Special Issue
Friction Determination by Atomic Force Microscopy in Field of Biochemical Science
Previous Article in Journal
FR4-Based Electromagnetic Scanning Micromirror Integrated with Angle Sensor
Previous Article in Special Issue
A Horizontal Magnetic Tweezers and Its Use for Studying Single DNA Molecules
Article Menu
Issue 5 (May) cover image

Export Article

Open AccessReview
Micromachines 2018, 9(5), 216; https://doi.org/10.3390/mi9050216

Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination

1
Biophotonics and Molecular Imaging Center, Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
2
Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
3
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
*
Authors to whom correspondence should be addressed.
Received: 15 March 2018 / Revised: 25 April 2018 / Accepted: 28 April 2018 / Published: 3 May 2018
(This article belongs to the Special Issue Micro Technologies for Single Molecule Manipulation and Detection)
  |  
PDF [2506 KB, uploaded 3 May 2018]
  |  

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 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. View Full-Text
Keywords: single molecule analysis; tethered particle motion; site-specific recombination; serine recombinases; tyrosine recombinases; Cre; Flp; ϕC31integrase single molecule analysis; tethered particle motion; site-specific recombination; serine recombinases; tyrosine recombinases; Cre; Flp; ϕC31integrase
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
SciFeed

Share & Cite This Article

MDPI and ACS Style

Fan, H.-F.; Ma, C.-H.; Jayaram, M. Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination. Micromachines 2018, 9, 216.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Micromachines EISSN 2072-666X Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top