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Van Loenhout, M.T. (author), De Vlaminck, I. (author), Flebus, B. (author), Den Blanken, J.F. (author), Zweifel, L.P. (author), Hooning, K.M. (author), Kerssemakers, J.W. (author), Dekker, C. (author)
The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that...
journal article 2013
document
De Vlaminck, I. (author), Henighan, T. (author), Van Loenhout, M.T.J. (author), Burnham, D.R. (author), Dekker, C. (author)
Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization...
journal article 2012
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De Vlaminck, I. (author), Van Loenhout, M.T.J. (author), Zweifel, L. (author), Den Blanken, J. (author), Hooning, K. (author), Hage, S. (author), Kerssemakers, J. (author), Dekker, C. (author)
In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule manipulation, combining...
journal article 2012
document
Van Loenhout, M.T.J. (author), Kerssemakers, J.W.J. (author), De Vlaminck, I. (author), Dekker, C. (author)
We present a three-dimensional tracking routine for nondiffraction-limited particles, which significantly reduces pixel bias. Our technique allows for increased resolution compared to that of previous methods, especially at low magnification or at high signal/noise ratio. This enables tracking with nanometer accuracy in a wide field of view and...
journal article 2012
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Holthausen, J.T. (author), Van Loenhout, M.T.J. (author), Sanchez, H. (author), Ristic, D. (author), Van Rossum-Fikkert, S.E. (author), Modesti, M. (author), Dekker, C. (author), Kanaar, R. (author), Wyman, C. (author)
Homologous recombination is essential for the preservation of genome stability, thereby preventing cancer. The recombination protein RAD51 drives DNA strand exchange, which requires the assembly, rearrangement and disassembly of a RAD51 filament on DNA, coupled to ATP binding and hydrolysis. This process is facilitated and controlled by...
journal article 2011
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De Vlaminck, I. (author), Vidic, I. (author), Van Loenhout, M.T.J. (author), Kanaar, R. (author), Lebbink, J.H.G. (author), Dekker, C. (author)
All cellular single-stranded (ss) DNA is rapidly bound and stabilized by single stranded DNA-binding proteins (SSBs). Replication protein A, the main eukaryotic SSB, is able to unwind double-stranded (ds) DNA by binding and stabilizing transiently forming bubbles of ssDNA. Here, we study the dynamics of human RPA (hRPA) activity on topologically...
journal article 2010
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Van Loenhout, M.T.J. (author), Van der Heijden, T. (author), Kanaar, R. (author), Wyman, C. (author), Dekker, C. (author)
RecA, the key protein in homologous recombination, performs its actions as a helical filament on single-stranded DNA (ssDNA). ATP hydrolysis makes the RecA–ssDNA filament dynamic and is essential for successful recombination. RecA has been studied extensively by single-molecule techniques on double-stranded DNA (dsDNA). Here we directly probe...
journal article 2009
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