Search Results - "Dekker, Nynke H"

Chromatin fibers stabilize nucleosomes under torsional stress by Kaczmarczyk, Artur, Meng, He, Ordu, Orkide, Noort, John van, Dekker, Nynke H.

“…Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of…”
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High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics by Dulin, David, Cui, Tao Ju, Cnossen, Jelmer, Docter, Margreet W., Lipfert, Jan, Dekker, Nynke H.

“…The observation of biological processes at the molecular scale in real time requires high spatial and temporal resolution. Magnetic tweezers are…”
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Single-molecule investigations of the stringent response machinery in living bacterial cells by English, Brian P, Hauryliuk, Vasili, Sanamrad, Arash, Tankov, Stoyan, Dekker, Nynke H, Elf, Johan

“…The RelA-mediated stringent response is at the heart of bacterial adaptation to starvation and stress, playing a major role in the bacterial cell cycle and…”
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Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments by Dekker, Nynke H, Lipfert, Jan, Kerssemakers, Jacob W J, Jager, Tessa

“…We introduce magnetic torque tweezers, which enable direct single-molecule measurements of torque. Our measurements of the effective torsional stiffness C of…”
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Origin of the electrophoretic force on DNA in solid-state nanopores by Lemay, Serge G, van Dorp, Stijn, Keyser, Ulrich F, Dekker, Nynke H, Dekker, Cees

“…Despite gel electrophoresis being one of the main workhorses of molecular biology, the physics of polyelectrolyte electrophoresis in a strongly confined…”
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Automated cell counting for Trypan blue-stained cell cultures using machine learning by Kuijpers, Louis, van Veen, Edo, van der Pol, Leo A, Dekker, Nynke H

“…Cell counting is a vital practice in the maintenance and manipulation of cell cultures. It is a crucial aspect of assessing cell viability and determining…”
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Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA by Lipfert, Jan, Skinner, Gary M., Keegstra, Johannes M., Hensgens, Toivo, Jager, Tessa, Dulin, David, Köber, Mariana, Yu, Zhongbo, Donkers, Serge P., Chou, Fang-Chieh, Das, Rhiju, Dekker, Nynke H.

“…Significance RNA, like DNA, can form double helices held together by the pairing of complementary bases, and such helices are ubiquitous in functional RNAs…”
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Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation by Ramírez Montero, Daniel, Sánchez, Humberto, van Veen, Edo, van Laar, Theo, Solano, Belén, Diffley, John F. X., Dekker, Nynke H.

“…The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of…”
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Studying genomic processes at the single-molecule level: introducing the tools and applications by Dulin, David, Lipfert, Jan, Moolman, M. Charl, Dekker, Nynke H.

“…Key Points We present key examples of the use of single-molecule approaches to study transcription, translation, splicing and replication. We highlight the…”
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Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids by Lipfert, Jan, Wiggin, Matthew, Kerssemakers, Jacob W.J., Pedaci, Francesco, Dekker, Nynke H.

“…The double-stranded nature of DNA links its replication, transcription and repair to rotational motion and torsional strain. Magnetic tweezers (MT) are a…”
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A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint by Sánchez, Humberto, Liu, Zhaowei, van Veen, Edo, van Laar, Theo, Diffley, John F. X., Dekker, Nynke H.

“…Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex…”
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CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands by Rouillon, Clément, Eckhardt, Bruna V, Kollenstart, Leonie, Gruss, Fabian, Verkennis, Alexander E E, Rondeel, Inge, Krijger, Peter H L, Ricci, Giulia, Biran, Alva, van Laar, Theo, Delvaux de Fenffe, Charlotte M, Luppens, Georgiana, Albanese, Pascal, Sato, Koichi, Scheltema, Richard A, de Laat, Wouter, Knipscheer, Puck, Dekker, Nynke H, Groth, Anja, Mattiroli, Francesca

“…Abstract During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key…”
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DNA replication origins retain mobile licensing proteins by Sánchez, Humberto, McCluskey, Kaley, van Laar, Theo, van Veen, Edo, Asscher, Filip M., Solano, Belén, Diffley, John F. X., Dekker, Nynke H.

“…DNA replication in eukaryotes initiates at many origins distributed across each chromosome. Origins are bound by the origin recognition complex (ORC), which,…”
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Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics by Ordu, Orkide, Kremser, Leopold, Lusser, Alexandra, Dekker, Nynke H

“…Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in…”
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Distinguishing Single- and Double-Stranded Nucleic Acid Molecules Using Solid-State Nanopores by Skinner, Gary M, van den Hout, Michiel, Broekmans, Onno, Dekker, Cees, Dekker, Nynke H

“…Solid-state nanopores offer a promising method for rapidly probing the structural properties of biopolymers such as DNA and RNA. We have for the first time…”
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Salt Dependence of Ion Transport and DNA Translocation through Solid-State Nanopores by Smeets, Ralph M. M, Keyser, Ulrich F, Krapf, Diego, Wu, Meng-Yue, Dekker, Nynke H, Dekker, Cees

“…We report experimental measurements of the salt dependence of ion transport and DNA translocation through solid-state nanopores. The ionic conductance shows a…”
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Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes by Vlijm, Rifka, Lee, Mina, Lipfert, Jan, Lusser, Alexandra, Dekker, Cees, Dekker, Nynke H.

“…DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to…”
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Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase by Dulin, David, Vilfan, Igor D., Berghuis, Bojk A., Hage, Susanne, Bamford, Dennis H., Poranen, Minna M., Depken, Martin, Dekker, Nynke H.

“…RNA viruses have specific mutation rates that balance the conflicting needs of an evolutionary response to host antiviral defenses and avoidance of the error…”
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Hysteresis in DNA compaction by Dps is described by an Ising model by Vtyurina, Natalia N., Dulin, David, Docter, Margreet W., Meyer, Anne S., Dekker, Nynke H., Abbondanzieri, Elio A.

“…In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of…”
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Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers by Dulin, David, Arnold, Jamie J., van Laar, Theo, Oh, Hyung-Suk, Lee, Cheri, Perkins, Angela L., Harki, Daniel A., Depken, Martin, Cameron, Craig E., Dekker, Nynke H.

“…RNA viruses pose a threat to public health that is exacerbated by the dearth of antiviral therapeutics. The RNA-dependent RNA polymerase (RdRp) holds promise…”
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