Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA

Autor: Jack W. Shepherd, Sebastien Guilbaud, Zhaokun Zhou, Jamieson A. L. Howard, Matthew Burman, Charley Schaefer, Adam Kerrigan, Clare Steele-King, Agnes Noy, Mark C. Leake

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)

Abstract Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures o

Externí odkaz: https://doaj.org/article/7db654a7a24440c7a4597f05ffd56ce8

Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy

Autor: Adam S. Backer, Jack W Shepherd, Iddo Heller, Graeme A. King, Mark C. Leake, Agnes Noy, Erwin J.G. Peterman, Andreas S. Biebricher, Gijs J.L. Wuite

Publikováno v: The Journal of Physical Chemistry. B
Journal of Physical Chemistry B, 125(30), 8351-8361. American Chemical Society
The Journal of Physical Chemistry
Backer, A S, King, G A, Biebricher, A S, Shepherd, J W, Noy, A, Leake, M C, Heller, I, Wuite, G J L & Peterman, E J G 2021, ' Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy ', Journal of Physical Chemistry B, vol. 125, no. 30, pp. 8351-8361 . https://doi.org/10.1021/acs.jpcb.1c02708

The combination of DNA force spectroscopy and polarization microscopy of fluorescent DNA intercalator dyes can provide valuable insights into the structure of DNA under tension. These techniques have previously been used to characterize S-DNA - an el

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b12a9fe28b567a6fb6bb03315b05d8a6
http://europepmc.org/articles/PMC8350907

PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data

Autor: Edward Higgins, Adam J. M. Wollman, Jack W Shepherd, Mark C. Leake

Publikováno v: Computational and Structural Biotechnology Journal, Vol 19, Iss, Pp 4049-4058 (2021)
Computational and Structural Biotechnology Journal

Graphical abstract
Highlights • We present PySTACHIO, a refined version of our spot tracking algorithm. • We demonstrate highly improved performance over previous MATLAB versions. • PySTACHIO can accurately estimate stoichiometries and 2D

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::45fd988c44bc1bf2a6f9a821a51ae9ea
http://www.sciencedirect.com/science/article/pii/S2001037021002944

Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: in vitro and in vivo

Autor: Sarah Lecinski, Jack W. Shepherd, Kate Bunting, Lara Dresser, Steven D. Quinn, Chris MacDonald, Mark C. Leake

In eukaryotes, intracellular physico-chemical properties like macromolecular crowding and cytoplasmic viscoelasticity influence key processes such as metabolic activities, molecular diffusion and protein folding. However, mapping crowding and viscoel

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bfb819d6cc13949e93fec1445c5a55a4
https://doi.org/10.1101/2022.06.27.497768

Localization Microscopy: A Review of the Progress in Methods and Applications

Autor: Jack W. Shepherd, Mark C. Leake

Publikováno v: Principles of Light Microscopy: From Basic to Advanced ISBN: 9783031044762

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ccef939ccbccd145aeaf1fde142248ca
https://doi.org/10.1007/978-3-031-04477-9_13