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Kim, S.H. (author), Ganji, M. (author), Kim, E. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes ...
journal article 2018
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Verschueren, D.V. (author), Pud, S. (author), Shi, X. (author), de Angelis, L. (author), Kuipers, L. (author), Dekker, C. (author)
Solid-state nanopores are single-molecule sensors that hold great potential for rapid protein and nucleic-acid analysis. Despite their many opportunities, the conventional ionic current detection scheme that is at the heart of the sensor suffers inherent limitations. This scheme intrinsically couples signal strength to the driving voltage,...
journal article 2018
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Caneva, S.L. (author), Gehring, P. (author), Suárez, Víctor García (author), García-Fuente, Amador (author), Stefani, D. (author), Olavarria Contreras, I.J. (author), Ferrer, Jaime (author), Dekker, C. (author), van der Zant, H.S.J. (author)
. Consistent with the principles of subwavelength optics, the wave nature of...
journal article 2018
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Yang, W.W.W. (author), Restrepo Perez, L. (author), Bengtson, M.L. (author), Heerema, S.J. (author), Birnie, A.T.F. (author), van der Torre, J. (author), Dekker, C. (author)
Solid-state nanopores have emerged as promising platforms for biosensing including diagnostics for disease detection. Here we show nanopore experiments that detect CRISPR-dCas9, a sequence-specific RNA-guided protein system that specifically binds to a target DNA sequence. While CRISPR-Cas9 is acclaimed for its gene editing potential, the...
journal article 2018
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Jansen, A.J. (author), Dekker, M.C. (author), van der Steen, Diederik (author)
Providing athletes with real-time feedback on their performance is becoming common in many sports, also in speed skating. This research-by-design project aims at finding a tool that allows the speed skater to get real-time feedback on his performance. Speed skaters often mention a so-called “good feeling” when skating behind a better skater. It...
conference paper 2018
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Fanalista, F. (author), Deshpande, S.R. (author), Lau, A.W.H.R. (author), Pawlik, G. (author), Dekker, C. (author)
Recently, both the cellular and synthetic biology communities have expressed a strong interest in coacervates, membrane‐less liquid droplets composed of densely packed multivalent molecules that form as a result of spontaneous phase separation. Here, it is studied how FtsZ, a protein that plays a key role in the bacterial division process,...
journal article 2018
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Dekker, Mark M. (author), van Lieshout, Rolf N. (author), Ball, Robin C. (author), Bouman, Paul C. (author), Dekker, Stefan C. (author), Dijkstra, Henk A. (author), Goverde, R.M.P. (author), Huisman, Dennis (author), Panja, Deb (author), Schaafsma, Alfons A.M. (author), van den Akker, Marjan (author)
Railway systems occasionally get into a state of out-of-control, meaning that there is barely any train is running, even though the required resources (infrastructure, rolling stock and crew) are available. These situations can either be caused by large disruptions or unexpected propagation and accumulation of delays. Because of the large number...
conference paper 2018
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Eeftens, J.M. (author), Dekker, C. (author)
Structural maintenance of chromosome (SMC) complexes are central regulators of chromosome architecture that are essential in all domains of life. For decades, the structural biology field has been debating how these conserved protein complexes use their intricate ring-like structures to structurally organize DNA. Here, we review the...
review 2017
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Berghuis, B.A. (author), Raducanu, Vlad-Stefan (author), Elshenawy, Mohamed M. (author), Jergic, S (author), Depken, S.M. (author), Dixon, NE (author), Hamdan, Samir M. (author), Dekker, N.H. (author)
Synchronizing the convergence of the two-oppositely moving DNA replication machineries at specific termination sites is a tightly coordinated process in bacteria. In Escherichia coli, a “replication fork trap” – found within a chromosomal region where forks are allowed to enter but not leave – is set by the protein–DNA roadblock Tus–Ter. The...
journal article 2017
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Terakawa, Tsuyoshi (author), Bisht, Shveta (author), Eeftens, J.M. (author), Dekker, C. (author), Haering, Christian H. (author), Greene, Eric C. (author)
Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. We used single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of adenosine triphosphate hydrolysis–dependent translocation along double-stranded DNA....
journal article 2017
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Restrepo Perez, L. (author), John, Shalini (author), Aksimentiev, Aleksei (author), Joo, C. (author), Dekker, C. (author)
Using nanopores for single-molecule sequencing of proteins – similar to nanopore-based sequencing of DNA – faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule...
journal article 2017
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Kabiri, Y. (author), Ananth, A.N. (author), van der Torre, J. (author), Katan, A.J. (author), Hong, Jin Yong (author), Malladi, S.R.K. (author), Kong, Jing (author), Zandbergen, H.W. (author), Dekker, C. (author)
While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported...
journal article 2017
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Neklyudova, M. (author), Erdamar, A.K. (author), Vicarelli, L. (author), Heerema, S.J. (author), Rehfeldt, T. (author), Pandraud, G. (author), Koladouz Esfahani, Z. (author), Dekker, C. (author), Zandbergen, H.W. (author)
We present a technique to fabricate ultrathin (down to 20 nm) uniform electron transparent windows at dedicated locations in a SiN membrane for in situ transmission electron microscopy experiments. An electron-beam (e-beam) resist is spray-coated on the backside of the membrane in a KOH-etched cavity in silicon which is patterned using...
journal article 2017
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Deshpande, S.R. (author), Birnie, A.T.F. (author), Dekker, C. (author)
Due to their cell membrane-mimicking properties, liposomes have served as a versatile research tool in science, from membrane biophysics and drug delivery systems to bottom-up synthetic cells. We recently reported a novel microfluidic method, Octanol-assisted Liposome Assembly (OLA), to form cell-sized, monodisperse, unilamellar liposomes...
journal article 2017
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Nechemia-Arbely, Yael (author), Fachinetti, Daniele (author), Miga, Karen H. (author), Sekulic, Nikolina (author), Soni, G.V. (author), Kim, Dong Hyun (author), Wong, Adeline K. (author), Lee, Ah Young (author), Nguyen, Kristen (author), Dekker, C. (author), Ren, Bing (author), Black, Ben E. (author), Cleveland, Don W. (author)
Chromatin assembled with centromere protein A (CENP-A) is the epigenetic mark of centromere identity. Using new reference models, we now identify sites of CENP-A and histone H3.1 binding within the megabase, α-satellite repeat-containing centromeres of 23 human chromosomes. The overwhelming majority (97%) of α-satellite DNA is found to be...
journal article 2017
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Vlijm, R. (author), Kim, S.H. (author), De Zwart, P. L. (author), Dalal, Y. (author), Dekker, C. (author)
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness...
journal article 2017
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Burnham, D.R. (author), Nijholt, B. (author), de Vlaminck, I. (author), Quan, Jinhua (author), Yusufzai, Timur (author), Dekker, C. (author)
We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant...
journal article 2017
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Shafqat, Salman (author), Hoefnagels, Johan P.M. (author), Savov, A.M. (author), Joshi, S. (author), Dekker, R. (author), Geers, Marc G.D. (author)
The exciting field of stretchable electronics (SE) promises numerous novel applications, particularly in-body and medical diagnostics devices. However, future advanced SE miniature devices will require high-density, extremely stretchable interconnects with micron-scale footprints, which calls for proven standardized (complementary metal-oxide...
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 Riessen, B. (author), Negenborn, R.R. (author), Dekker, Rommert (author)
The intermodal hinterland transportation of maritime containers is under pressure from port authorities and shippers to achieve a more integrated, efficient network operation. Current optimisation methods in literature yield limited results in practice, though, as the transportation product structure limits the flexibility to optimise network...
journal article 2017
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