Topoisomerases and ligases
Vaccinia virus and human Topoisomerase I
We study the mechanism of action of eukaryotic topoisomerase I enzymes (Top1B). Topoisomerases are enzymes that can change the degree of DNA supercoiling (over- or underwinding of the helical double-stranded DNA duplex) and are important and often vital during cell processes such as DNA replication and transcription.
We have studied Top1B from the vaccinia poxvirus and the Top1B from humans using magnetic tweezers. This technique allows one to dictate and monitor the topological state of an individual DNA molecule with high precision in real-time, which is achieved by stretching and twisting the DNA molecule by means of a pair of magnets and a magnetic particle attached to the DNA molecule. Using magnetic tweezers, we monitor in real-time how the topological state of the DNA molecule is affected by the Top1B.
Human Topoisomerase I poisoning by chemotherapeutic drugs
The camptothecin class of chemotherapeutic drugs are chemical agents that poison human Top1B. We study by what mechanism a member of the camptothecin class (topotecan) interferes with the Top1B-mediated supercoil relaxation at the single-molecule level. In addition, we test the implications of our single-molecule findings in vivo in the context of a yeast cell.
Current Researchers
Current Collaborations
- Mary-Ann Bjornsti, St. Judes Children's Research Hospital, Memphis, TN
- Chis Wiggins, Columbia University, New-York, NY
Previous contributions from
- Aurelien Crut
- Daniel Koster
- The Shuman group at the Sloan-Kettering Institute, New York
- Fernando Moreno-Herrero
- Elisa Bot
- Laurent Holtzer
- Vincent Croquette
- Cees Dekker
Publications
"Single-molecule observations of topotecan-mediated Top1B activity at a unique DNA sequence", D.A. Koster, F. Czerwinski, L. Halby, A. Crut, P. Vekhoff, K. Palle, P. B. Arimondo, and N.H. Dekker, Nucleic Acids Research, doi:10.1093/nar/gkn035 (2008)
"Antitumour drugs impede DNA uncoiling by Topoisomerase I", Daniel A. Koster, Komaraiah Palle, Elisa S.M. Bot, Mary-Ann Bjornsti, and Nynke H. Dekker, Nature 448:213-7 (2007)
“Multiple events on single molecules: unbiased estimation in single-molecule biophysics” , D.A. Koster, C. Wiggins, and N.H. Dekker, Proc. Natl. Acad. Sci. USA, 103, 1750-1755 (2006).
"Atomic force microscopy shows that vaccinia topoisomerase 1B forms filaments in a cooperative fashion”, F. Moreno-Herrero, L. Holtzer, D.A. Koster, S. Shuman, C. Dekker, and N.H. Dekker, Nucleic Acids Research 33, 5945 -5953 (2005).
"Friction and Torque Govern the Relaxation of DNA Supercoils by Eukaryotic Topoisomerase IB’’, D.A. Koster, V. Croquette, C. Dekker, S. Shuman, and N.H. Dekker, Nature 434, 671-674 (2005).
"Thermophilic Topoisomerase I on a Single DNA Molecule", N. H. Dekker, T. Viard, M. Duguet, V. Rybenkov, D. Bensimon, V. Croquette, J. Mol. Biol. 329, 271-282 (2003).
"The Mechanism of Type IA Topoisomerases", N. H. Dekker, V. V. Rybenkov, M. Duguet, N. J. Crisona, N. R. Cozzarelli, D. Bensimon, and V. Croquette, Proc. Natl. Acad. Sci. (USA) 99, 12126-12131 (2002).
“Tracking enzymatic steps of DNA topoisomerases using single-molecule micromanipulation”, T.R. Strick, G. Charvin, N.H. Dekker, J.-F. Allemand, D. Bensimon, and V. Croquette, C. R. Physique 3 (2002), 595-618.
