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Fragasso, A. (author), Schmid, S. (author), Dekker, C. (author)Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of...review 2020
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van Wee, R.G. (author), Filius, M. (author), Joo, C. (author)Single-molecule localization microscopy (SMLM) is a potent tool to examine biological systems with unprecedented resolution, enabling the investigation of increasingly smaller structures. At the forefront of these developments is DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT), which exploits the stochastic and...review 2021
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Tišma, M. (author), Kaljević, Jovana (author), Gruber, Stephan (author), Le, Tung B.K. (author), Dekker, C. (author)Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome...review 2024
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Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have...review 2023
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Severins, I.W.H. (author), Joo, C. (author), van Noort, John (author)Next-generation sequencing techniques have led to a new quantitative dimension in the biological sciences. In particular, integrating sequencing techniques with biophysical tools allows sequence-dependent mechanistic studies. Using the millions of DNA clusters that are generated during sequencing to perform high-throughput binding affinity...review 2022
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Ploetz, Evelyn (author), Ambrose, Benjamin (author), Barth, A. (author), Börner, Richard (author), Kapanidis, Achillefs N. (author), Lohman, Timothy M. (author), Steffen, Fabio D. (author), Cordes, Thorben (author), Magennis, Steven W. (author), Lerner, Eitan (author)PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is...review 2023
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Srivastava, Akshat (author)Single Molecule Localization Microscopy (SMLM) has enabled researchers to breakthrough the diffraction limit and obtain nanometer resolution images of macromolecular structures. But due to the time involved in obtaining ample data for proper image, the technique is venerable to many problem including fluctuations due to thermal gradients from...master thesis 2022
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van Dijk, Raymond (author)The microscope is an essential tool for biologists. Since the late 16th century, it has given researchers a better understanding of cell processes and greatly advanced healthcare. In this century, Single molecule localization microscopy (SMLM) has revolutionized optical microscopy by breaking the optical diffraction limit. Sparsely activating...master thesis 2022
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Houwink, Quint (author)Optical microscopes are fundamentally limited to a resolution of several hundreds of nanometers by the diffraction of light. Single-molecule localization microscopy (SMLM) circumvents this limit by sparsely exciting fluorescent molecules at different time instances. Single molecules can subsequently be localized with improved precision over the...master thesis 2021
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Shan, Jichao (author)Proteins play a key role in many biological processes and are thus useful indicators of health and disease states. Since the size of proteins is few hundred nanometers, it is necessary to explore new techniques to manipulate and 'read' them. This thesis aims to identify and build a platform that enables sub-micron bead manipulation, which will...master thesis 2022
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Perrin, M.L. (author), Martin, C.A. (author), Prins, F. (author), Shaikh, A.J. (author), Eelkema, R. (author), Van Esch, J.H. (author), Van Ruitenbeek, J.M. (author), Van der Zant, H.S. (author), Dulic, D. (author)We have investigated charge transport in ZnTPPdT-Pyr (TPPdT: 5,15-di(p-thiolphenyl)-10,20-di(p-tolyl)porphyrin) molecular junctions using the lithographic mechanically controllable break-junction (MCBJ) technique at room temperature and cryogenic temperature (6 K). We combined low-bias statistical measurements with spectroscopy of the molecular...journal article 2011
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Seidel, R. (author), Bloom, J.G.P. (author), Dekker, C. (author), Szczelkun, M.D. (author)The Type I restriction-modification enzyme EcoR124I is an archetypical helicase-based dsDNA translocase that moves unidirectionally along the 3'–5' strand of intact duplex DNA. Using a combination of ensemble and single-molecule measurements, we provide estimates of two physicochemical constants that are fundamental to a full description of...journal article 2008
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- Dekker, C. (author), Tans, S.J. (author), Geerligs, L.J. (author), Bezryadin, A. (author), Wu, J. (author), Wegner, G. (author) journal article 1997
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- Bezryadin, A. (author), Dekker, C. (author) journal article 1997
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Dange, T. (author), Joseph, A. (author), Grünwald, D. (author)Cellular life can be described as a dynamic equilibrium of a highly complex network of interacting molecules. For this reason, it is no longer sufficient to “only” know the identity of the participants in a cellular process, but questions such as where, when, and for how long also have to be addressed to understand the mechanism being...journal article 2010
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Frisenda, R. (author), Parlato, L. (author), Barra, M. (author), Van der Zant, H.S.J. (author), Cassinese, A. (author)In this letter, we report the single-molecule conductance properties of a cyano-functionalized perylene-diimide derivative (PDI8-CN 2 ) investigated with gold nano-electrodes. This molecule is of large interest for the fabrication of high-performance and air-stable n-type organic field-effect transistors. Low-bias experiments performed on...journal article 2015
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Löschberger, A. (author), Van de Linde, S. (author), Debauvalle, M.C. (author), Rieger, B. (author), Heilemann, M. (author), Krohne, G. (author), Sauer, M. (author)One of the most complex molecular machines of cells is the nuclear pore complex (NPC), which controls all trafficking of molecules in and out of the nucleus. Because of their importance for cellular processes such as gene expression and cytoskeleton organization, the structure of NPCs has been studied extensively during the last few decades,...journal article 2012
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Rubio-Bollinger, G. (author), Castellanos-Gomez, A. (author), Bilan, S. (author), Zotti, L.A. (author), Arroyo, C.R. (author), Agraït, N. (author), Cuevas, J. (author)We fabricate and characterize carbon-fiber tips for their use in combined scanning tunneling and force microscopy based on piezoelectric quartz tuning fork force sensors. An electrochemical fabrication procedure to etch the tips is used to yield reproducible sub-100-nm apex. We also study electron transport through singlemolecule junctions...journal article 2012
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Frisenda, R. (author), Tarkuc, S. (author), Galan, E. (author), Perrin, M.L. (author), Eelkema, R. (author), Grozema, F.C. (author), Van der Zant, H.S.J. (author)We report on an experimental investigation of transport through single molecules, trapped between two gold nano-electrodes fabricated with the mechanically controlled break junction (MCBJ) technique. The four molecules studied share the same core structure, namely oligo(phenylene ethynylene) (OPE3), while having different aurophilic anchoring...journal article 2015
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Kim, B. (author), Ha, M. (author), Loeff, L. (author), Chang, H. (author), Simanshu, D.K. (author), Li, S. (author), Fareh, M. (author), Patel, D.J. (author), Joo, C. (author), Kim, V.N. (author)Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the...journal article 2015