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van Oene, M.M. (author), Ha, S. (author), Jager, T. (author), Lee, M. (author), Pedaci, F. (author), Lipfert, J. (author), Dekker, N.H. (author)
Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and...
journal article 2018
document
van Oene, M.M. (author), Dickinson, L.E. (author), Cross, B. (author), Pedaci, F. (author), Lipfert, J. (author), Dekker, N.H. (author)
The bacterial flagellar motor of Escherichia coli is a nanoscale rotary engine essential for bacterial propulsion. Studies on the power output of single motors rely on the measurement of motor torque and rotation under external load. Here, we investigate the use of magnetic tweezers, which in principle allow the application and active control...
journal article 2017
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Kriegel, Franziska (author), Ermann, Niklas (author), Forbes, R.J.G. (author), Dulin, D. (author), Dekker, N.H. (author), Lipfert, J. (author)
The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. Many properties of DNA depend on the ionic environment due to its highly charged backbone. In particular, both theoretical analyses and direct singlemolecule experiments have shown its...
journal article 2017
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Van Oene, M.M. (author), Dickinson, L.E. (author), Pedaci, F. (author), Köber, M. (author), Dulin, D. (author), Lipfert, J. (author), Dekker, N.H. (author)
Superparamagnetic beads are widely used in biochemistry and single-molecule biophysics, but the nature of the anisotropy that enables the application of torques remains controversial. To quantitatively investigate the torques experienced by superparamagnetic particles, we use a biological motor to rotate beads in a magnetic field and demonstrate...
journal article 2015
document
Vlijm, R. (author), Lee, M. (author), Lipfert, J. (author), Lusser, A. (author), Dekker, C. (author), Dekker, N.H. (author)
DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length of single DNA molecules, we monitor the real...
journal article 2015
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Lipfert, J. (author), van Oene, M.M. (author), Lee, M. (author), Pedaci, F. (author), Dekker, N.H. (author)
journal article 2015
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Lee, M. (author), Lipfert, J. (author), Sanchez, H. (author), Wyman, C. (author), Dekker, N.H. (author)
Human RAD51 is a key protein in the repair of DNA by homologous recombination. Its assembly onto DNA, which induces changes in DNA structure, results in the formation of a nucleoprotein filament that forms the basis of strand exchange. Here, we determine the structural and mechanical properties of RAD51-dsDNA filaments. Our measurements use two...
journal article 2013
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Dulin, D. (author), Lipfert, J. (author), Moolman, M.C. (author), Dekker, N.H. (author)
To understand genomic processes such as transcription, translation or splicing, we need to be able to study their spatial and temporal organization at the molecular level. Single-molecule approaches provide this opportunity, allowing researchers to monitor molecular conformations, interactions or diffusion quantitatively and in real time in...
journal article 2013
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Lipfert, J. (author), Kerssemakers, J.J.W. (author), Rojer, M. (author), Dekker, N.H. (author)
The double helical nature of DNA links many cellular processes such as DNA replication, transcription, and repair to rotational motion and the accumulation of torsional strain. Magnetic tweezers (MTs) are a single-molecule technique that enables the application of precisely calibrated stretching forces to nucleic acid tethers and to control...
journal article 2011
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Lipfert, J. (author), Klijnhout, S. (author), Dekker, N.H. (author)
DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove binding anti-microbial drug; and topotecan, a...
journal article 2010
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