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Ornago, L. (author)In this dissertation, we analyse the charge transport of nanoscale molecular junctions in mechanically controllable break junction (MCBJ) experiments. In particular, we focus on the characterization of molecular features going beyond the "single-peak" picture, that is, considering features in the measurements in addition to themost prominent one...doctoral thesis 2023
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Mc Cluskey, K.A. (author), Dekker, N.H. (author)TIRF (Total Internal Reflection Fluorescence) microscopy is a powerful tool for measuring the intra- and intermolecular dynamics of fluorescently-labeled single molecules. As TIRF measurements move to more complex biological systems with more fluorescent probes, the multi-band-pass dichroic that separates excitation from emission becomes...journal article 2023
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Hsu, C. (author)This dissertation presents the experimental work on singlemolecule charge transport, particularly on the aspects of spin and orbital conformational effects in singlemolecule junctions. In this dissertation, we employ and develop various singlemolecule techniques, the mechanically controlled break junction (MCBJ), thermoelectric electromigrated...doctoral thesis 2022
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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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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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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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Filius, M. (author)Proteins are the workhorses of the cell, as such, they form the basis of all living systems. In order to fully understand biological processes, the ability to identify and quantify the proteins in cells is crucial. Identification can be achieved by determining the amino acid sequence of proteins, since this sequence is unique for each protein....doctoral thesis 2022
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Janissen, R. (author), Eslami Mossallam, B. (author), Artsimovitch, Irina (author), Depken, S.M. (author), Dekker, N.H. (author)Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high...journal article 2022
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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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Wen, C. (author), Bertosin, E. (author), Shi, X. (author), Dekker, C. (author), Schmid, Sonja (author)Nanopores are versatile single-molecule sensors offering a simple label-free readout with great sensitivity. We recently introduced the nanopore electro-osmotic trap (NEOtrap) which can trap and sense single unmodified proteins for long times. The trapping is achieved by the electro-osmotic flow (EOF) generated from a DNA-origami sphere...journal article 2022
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Kuijpers, L.C. (author), van Laar, T. (author), Janissen, R. (author), Dekker, N.H. (author)Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases with MT. We describe the preparation of a dsRNA construct for probing...journal article 2022
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Hulleman, C.N. (author)<i>Localization microscopy has circumvented the diffraction limit by sequentially</i> imaging individual light emitting molecules at a time. The position of these individual molecules can be determined and a super-resolution reconstruction is made with improved resolution. Normally freely rotating emitters are used such that the point spread...doctoral thesis 2021
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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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Seifert, Mona (author), Bera, Subhas C. (author), van Nies, Pauline (author), Kirchdoerfer, Robert N. (author), Shannon, Ashleigh (author), Le, Thi Tuyet Nhung (author), Meng, Xiangzhi (author), Depken, S.M. (author), Dulin, David (author)The absence of 'shovel-ready' anti-coronavirus drugs during vaccine development has exceedingly worsened the SARS-CoV-2 pandemic. Furthermore, new vaccine-resistant variants and coronavirus outbreaks may occur in the near future, and we must be ready to face this possibility. However, efficient antiviral drugs are still lacking to this day,...journal article 2021
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Bera, Subhas Chandra (author), Seifert, Mona (author), Kirchdoerfer, Robert N. (author), van Nies, Pauline (author), Wubulikasimu, Yibulayin (author), Quack, Salina (author), Papini, Flávia S. (author), Depken, S.M. (author), Dulin, D. (author)Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We use a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core...journal article 2021
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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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Navikas, Vytautas (author), Descloux, Adrien C. (author), Grußmayer, K.S. (author), Marion, Sanjin (author), Radenovic, Aleksandra (author)A variety of modern super-resolution microscopy methods provide researchers with previously inconceivable biological sample imaging opportunities at a molecular resolution. All of these techniques excel at imaging samples that are close to the coverslip, however imaging at large depths remains a challenge due to aberrations caused by the...journal article 2021
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Filius, M. (author), Kim, S.H. (author), Severins, I.W.H. (author), Joo, C. (author)Single-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only a couple of FRET pairs can be reliably measured on a single object, which makes it difficult to apply single-molecule FRET for structural analysis of biomolecules. Here, we present an approach that allows for the...journal article 2021
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Loeff, L. (author), Kerssemakers, J.W.J. (author), Joo, C. (author), Dekker, C. (author)Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step...journal article 2021
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de Bruijckere, J. (author)In this thesis we study charge transport through individual molecules and mainly focus on the properties of molecular spin. We fabricate nanoscale structures for transport measurements and employ the electromigration break-junction technique to realize three-terminal—transistor-like—single-molecule devices. We investigate the spin-related...doctoral thesis 2020