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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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Moolman, M.C. (author), Huang, Z. (author), Krishnan, S.T. (author), Kerssemakers, J.W.J. (author), Dekker, N.H. (author)Background: Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this...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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Pedaci, F. (author), Huang, Z. (author), Van Oene, M. (author), Dekker, N.H. (author)The optical torque wrench is a laser trapping technique that expands the capability of standard optical tweezers to torque manipulation and measurement, using the laser linear polarization to orient tailored microscopic birefringent particles. The ability to measure torque of the order of kBT (?4 pN nm) is especially important in the study of...journal article 2012
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Dekker, N.H. (author), Pedaci, F. (author), Barland, S. (author)The invention provides a method for sensing with a sensor system an analyte in an analyte fluid. The sensor system comprises a micron scale birefringent entity, a laser unit configured to generate polarized laser light, a polarization rotation device, wherein the laser unit and polarization rotation device are configured to rotate at a...patent 2012
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Dekker, N.H. (author), Kerssemakers, J. (author), Lipfert, J. (author)The invention concerns a method and apparatus for determining one or more characterizing features of a macromolecule, in particular torque and/or twist of nucleic acids like DNA, using magnetic fields.patent 2011
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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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Van den Hout, M. (author), Hall, A.R. (author), Wu, M.Y. (author), Zandbergen, H.W. (author), Dekker, C. (author), Dekker, N.H. (author)Solid-state nanopores are considered a promising tool for the study of biological polymers such as DNA and RNA, due largely to their flexibility in size, potential in device integration and robustness. Here, we show that the precise shape of small nanopores (?5 nm diameter in 20 nm SiN membranes) can be controlled by using transmission electron...journal article 2010
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Smeets, R.M.M. (author), Dekker, N.H. (author), Dekker, C. (author)Low-frequency ionic current noise in solid-state nanopores imposes a limitation on the time resolution achieved in translocation experiments. Recently, this 1/ f noise was described as obeying Hooge’s phenomenological relation, where the noise scales inversely with the number of charge carriers present. Here, we consider an alternative model in...journal article 2009
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Vilfan, I.D. (author), Candelli, A. (author), Hage, S. (author), Aalto, A.P. (author), Poranen, M.M. (author), Bamford, D.H. (author), Dekker, N.H. (author)RNA-dependent RNA polymerases (RdRP) form an important class of enzymes that is responsible for genome replication and transcription in RNA viruses and involved in the regulation of RNA interference in plants and fungi. The RdRP kinetics have been extensively studied, but pausing, an important regulatory mechanism for RNA polymerases that has...journal article 2008
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- Crut, A. (author), Koster, D.A. (author), Huang, Z. (author), Hage, S. (author), Dekker, N.H. (author) journal article 2008
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Koster, D.A. (author), Czerwinski, F. (author), Halby, L. (author), Crut, A. (author), Vekhoff, P. (author), Palle, K. (author), Arimondo, P.B. (author), Dekker, N.H. (author)The rate of DNA supercoil removal by human topoisomerase IB (TopIB) is slowed down by the presence of the camptothecin class of antitumor drugs. By preventing religation, these drugs also prolong the lifetime of the covalent TopIB–DNA complex. Here, we use magnetic tweezers to measure the rate of supercoil removal by drugbound TopIB at a single...journal article 2008
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Van den Hout, M. (author), Hage, S. (author), Dekker, C. (author), Dekker, N.H. (author)Many experiments involving nucleic acids require the hybridization and ligation of multiple DNA or RNA molecules to form a compound molecule. When one of the constituents is single stranded, however, the efficiency of ligation can be very low and requires significant individually tailored optimization. Also, when the molecules involved are very...journal article 2008
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Vilfan, I.D. (author), Candelli, A. (author), Hage, S. (author), Aalto, A.P. (author), Poranen, M.M. (author), Bamford, D.H. (author), Dekker, N.H. (author)RNA-dependent RNA polymerases (RdRP) form an important class of enzymes that is responsible for genome replication and transcription in RNA viruses and involved in the regulation of RNA interference in plants and fungi. The RdRP kinetics have been extensively studied, but pausing, an important regulatory mechanism for RNA polymerases that has...journal article 2008
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Vilfan, I.D. (author), Kamping, W. (author), Van den Hout, M. (author), Candelli, A. (author), Hage, S. (author), Dekker, N.H. (author)Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNAenzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several...journal article 2007
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- Besteman, K. (author), Hage, S. (author), Dekker, N.H. (author), Lemay, G. (author) journal article 2007
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- Smeets, R.M.M. (author), Keyser, U.F. (author), Wu, M.Y. (author), Dekker, N.H. (author), Dekker, C. (author) journal article 2006
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- Koster, D.A. (author), Wiggins, C.H. (author), Dekker, N.H. (author) journal article 2006
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- Moreno-Herrero, F. (author), Seidel, R. (author), Johnson, S.M. (author), Fire, A. (author), Dekker, N.H. (author) journal article 2006