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Tang, Yuchen (author)Rivers are vital for maintaining freshwater ecosystems as they distribute nutrients as well as dilute and transport anthropogenic pollution. Tracers provide direct empirical data on complex waterflows and reveal transport processes of waterborne substances. Recent advances in material engineering and biomolecular technology have made it possible...doctoral thesis 2023
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Tang, Yuchen (author), van Rhijn, Fay (author), Abdelrady, Ahmed (author), Foppen, J.W.A. (author), Bogaard, T.A. (author)Recently, superparamagnetic silica encapsulated DNA microparticles (SiDNAFe) were designed and in various experiments used as a hydrological tracer. We investigated the effect of bed characteristics on the transport behaviour and especially the mass loss of SiDNAFe in open channel injection experiments. Hereto, a series of laboratory...journal article 2023
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Foppen, J.W.A. (author)The use of artificial DNA (artDNA) in hydrological applications is becoming increasingly popular, either in dissolved form (dissolved artDNA) or encapsulated and protected by a layer (encDNA). DNA can be detected even at low concentrations and offers the ability to create numerous uniquely identifiable DNA labels, making it ideal for a wide...review 2023
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Yang, Shuo (author), Joesaar, A.H. (author), Bögels, Bas W.A. (author), Mann, Stephen (author), de Greef, Tom F.A. (author)Protocells containing enzyme-driven biomolecular circuits that can process and exchange information offer a promising approach for mimicking cellular features and developing molecular information platforms. Here, we employ synthetic transcriptional circuits together with CRISPR/Cas-based DNA processing inside semipermeable protein-polymer...journal article 2022
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Ganguly, Amlan (author), Abadal, Sergi (author), Thakkar, Ishan (author), Enright Jerger, Natalie (author), Riedel, Marc (author), Babaie, M. (author), Balasubramonian, Rajeev (author), Sebastian, Abu (author), Pasricha, Sudeep (author), Taskin, Baris (author)The computing world is witnessing a proverbial Cambrian explosion of emerging paradigms propelled by applications, such as artificial intelligence, big data, and cybersecurity. The recent advances in technology to store digital data inside a deoxyribonucleic acid (DNA) strand, manipulate quantum bits (qubits), perform logical operations with...journal article 2022
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Holub, M. (author), Birnie, A.T.F. (author), Japaridze, A. (author), van der Torre, J. (author), Ridder, Maxime den (author), de Ram, C. (author), Pabst, Martin (author), Dekker, C. (author)Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the...journal article 2022
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Tang, Yuchen (author), Foppen, J.W.A. (author), Bogaard, T.A. (author)Surface water tracing is a widely used technique to investigate in-stream mass transport including contaminant migration. Recently, a microparticle tracer was developed with unique synthetic DNA encapsulated in an environmentally-friendly silica coating (Si-DNA microparticle). Previous tracing applications of such tracers reported detection...journal article 2021
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Birnie, Anthony (author), Dekker, C. (author)Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics,...review 2021
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Cui, T.J. (author)In this thesis we used single-molecule FRET to investigate the kinetic properties of a protein called Argonaute. While traditionally one uses bulk methods to investigate the molecular properties of proteins, bulk methods do not confer information that is transient, since that is inherently averaged out. Single-molecule methods, as their name...doctoral thesis 2019
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Globyte, V. (author)The most commonly known relationship between the macromolecules of life – DNA, RNA and protein – is the central dogma which states that information flows from DNA to RNA through transcription and from RNA to protein through translation. The discovery of non-coding RNAs has altered and expanded this picture by revealing many more functions of RNA...doctoral thesis 2019
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Kabiri, Y. (author), Angelin, Alessandro (author), Ahmed, Ishtiaq (author), Mutlu, Hatice (author), Bauer, Jens (author), Niemeyer, Christof M. (author), Zandbergen, H.W. (author), Dekker, C. (author)Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR...journal article 2019
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Damsteeg-van Berkel, Selma (author), Beemster, Fleur (author), Dankelman, J. (author), Loeve, A.J. (author)Purpose: DNA is a highly valuable lead to identify people who were possibly involved in a crime. Even by small contact events, minute amounts of DNA (‘trace DNA’) can be transferred from a DNA source to an evidentiary item, which can be enough for a successful DNA analysis. The focus of this research is to get more insight in the collection...journal article 2019
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Iashina, Ekaterina G. (author), Filatov, Mikhail V. (author), Pantina, Rimma A. (author), Varfolomeeva, Elena Y. (author), Bouwman, W.G. (author), Duif, C.P. (author), Honecker, Dirk (author), Pipich, Vitaliy (author), Grigoriev, Sergey V. (author)This paper reports on the two-scale fractal structure of chromatin organization in the nucleus of the HeLa cell. Two neutron scattering methods, small-angle neutron scattering (SANS) and spin-echo SANS, are used to unambiguously identify the large-scale structure as being a logarithmic fractal with the correlation function (r) - ln(r/E). The...journal article 2019
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Langstraat, Kirsten (author), Knijnenberg, Alwin (author), Edelman, Gerda (author), Van De Merwe, Linda (author), van Loon, A. (author), Dik, J. (author), van Asten, Arian C. (author)This study introduces the use of macroscopic X-ray fluorescence (MA-XRF) for the detection, classification and imaging of forensic traces over large object areas such as entire pieces of clothing and wall paneling. MA-XRF was sufficiently sensitive and selective to detect human biological traces like blood, semen, saliva, sweat and urine on...journal article 2017
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)DNA read alignment is a major step in genome analysis. However, as DNA reads continue to become longer, new approaches need to be developed to effectively use these longer reads in the alignment process. Modern aligners commonly use a two-step approach for read alignment: 1. seeding, 2. extension. In this paper, we have investigated various...conference paper 2016
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Rems, L. (author), Kawale, D. (author), James Lee, L. (author), Boukany, P. (author)Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new singlemolecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena,...journal article 2016
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Salari, H. (author), Eslami-Mossallam, B. (author), Nederi, S. (author), Ejtehadi, M.R. (author)Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length...journal article 2015
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Plesa, C. (author)Solid-state nanopores are small nanometer-scale holes in thin membranes. When used to separate two chambers containing salt solution, any biomolecule passing from one chamber to the other is forced to pass through the pore constriction. An electric field applied across the membrane is used to create an ionic current and electrophoretically drive...doctoral thesis 2015
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Vlijm, R. (author)The main focus of this thesis is a better understanding of the basic compaction mechanism of our DNA using multiple single-molecule techniques. The stretched-out length of our DNA is enormous compared with the dimensions of a cell. To make DNA fit within a cell it is systematically wrapped around proteins (histone octamers), forming nucleosomes....doctoral thesis 2014
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Van Loenhout, M.T.J. (author)This thesis describes a series of single-molecule experiments aimed at understanding the physical properties of DNA itself and the proteins that interact with it. We developed and applied sensitive techniques that allowed us to directly probe the conformation and interactions of individual DNA molecules and proteins. Magnetic and optical...doctoral thesis 2012
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