Skip to main content
Home
Department Of Physics text logo
  • Research
    • Our research
    • Our research groups
    • Our research in action
    • Research funding support
    • Summer internships for undergraduates
  • Study
    • Undergraduates
    • Postgraduates
  • Engage
    • For alumni
    • For business
    • For schools
    • For the public
Menu
CMP
Credit: Jack Hobhouse

Professor Achillefs Kapanidis

Professor of Biological Physics

Research theme

  • Biological physics

Sub department

  • Condensed Matter Physics

Research groups

  • Gene machines
Achillefs.Kapanidis@physics.ox.ac.uk
Telephone: 01865 (2)72226
Biochemistry Building
groups.physics.ox.ac.uk/genemachines/group
  • About
  • Publications

Tethered fluorophore motion: studying large DNA conformational changes by single-fluorophore imaging.

Biophysical journal Elsevier 107:5 (2014) 1205-1216

Authors:

PF May, JN Pinkney, P Zawadzki, GW Evans, DJ Sherratt, AN Kapanidis

Abstract:

We have previously introduced tethered fluorophore motion (TFM), a single-molecule fluorescence technique that monitors the effective length of a biopolymer such as DNA. TFM uses the same principles as tethered particle motion (TPM) but employs a single fluorophore in place of the bead, allowing TFM to be combined with existing fluorescence techniques on a standard fluorescence microscope. TFM has been previously been used to reveal the mechanism of two site-specific recombinase systems, Cre-loxP and XerCD-dif. In this work, we characterize TFM, focusing on the theoretical basis and potential applications of the technique. Since TFM is limited in observation time and photon count by photobleaching, we present a description of the sources of noise in TFM. Comparing this with Monte Carlo simulations and experimental data, we show that length changes of 100 bp of double-stranded DNA are readily distinguishable using TFM, making it comparable with TPM. We also show that the commonly recommended pixel size for single-molecule fluorescence approximately optimizes signal to noise for TFM experiments, thus enabling facile combination of TFM with other fluorescence techniques, such as Förster resonance energy transfer (FRET). Finally, we apply TFM to determine the polymerization rate of the Klenow fragment of DNA polymerase I, and we demonstrate its combination with FRET to observe synapsis formation by Cre using excitation by a single laser. We hope that TFM will be a useful addition to the single-molecule toolkit, providing excellent insight into protein-nucleic acid interactions.
More details from the publisher
Details from ORA
More details
More details

Single-molecule FRET reveals a corkscrew RNA structure for the polymerase-bound influenza virus promoter

Proceedings of the National Academy of Sciences of the United States of America Proceedings of the National Academy of Sciences 111:32 (2014) e3335-e3342

Authors:

Alexandra I Tomescu, Nicole C Robb, Narin Hengrung, Ervin Fodor, Achillefs N Kapanidis
More details from the publisher
More details
More details

Studying the organization of DNA repair by single-cell and single-molecule imaging

DNA Repair Elsevier 20:100 (2014) 32-40

Authors:

Stephan Uphoff, Achillefs N Kapanidis
More details from the publisher
More details
More details

Characterization of organic fluorophores for in vivo FRET studies based on electroporated molecules

Physical Chemistry Chemical Physics Royal Society of Chemistry (RSC) 16:25 (2014) 12688-12694

Authors:

A Plochowietz, R Crawford, AN Kapanidis
More details from the publisher
More details
More details

Optimized delivery of fluorescently labeled proteins in live bacteria using electroporation

Histochemistry and Cell Biology Springer Nature 142:1 (2014) 113-124

Authors:

Marko Sustarsic, Anne Plochowietz, Louise Aigrain, Yulia Yuzenkova, Nikolay Zenkin, Achillefs Kapanidis
More details from the publisher
More details
More details

Pagination

  • First page First
  • Previous page Prev
  • …
  • Page 18
  • Page 19
  • Page 20
  • Page 21
  • Current page 22
  • Page 23
  • Page 24
  • Page 25
  • Page 26
  • …
  • Next page Next
  • Last page Last

Footer Menu

  • Contact us
  • Giving to the Dept of Physics
  • Work with us
  • Media

User account menu

  • Log in

Follow us

FIND US

Clarendon Laboratory,

Parks Road,

Oxford,

OX1 3PU

CONTACT US

Tel: +44(0)1865272200

University of Oxfrod logo Department Of Physics text logo
IOP Juno Champion logo Athena Swan Silver Award logo

© University of Oxford - Department of Physics

Cookies | Privacy policy | Accessibility statement

Built by: Versantus

  • Home
  • Research
  • Study
  • Engage
  • Our people
  • News & Comment
  • Events
  • Our facilities & services
  • About us
  • Current students
  • Staff intranet