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Sökning: WFRF:(Fritzsche Joachim)

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31.
  • Iarko, V., et al. (författare)
  • Extension of nanoconfined DNA: Quantitative comparison between experiment and theory
  • 2015
  • Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755 .- 1550-2376. ; 92:6, s. Art. Nr. 062701-
  • Tidskriftsartikel (refereegranskat)abstract
    • The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
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32.
  • Kesarimangalam, Sriram, 1983, et al. (författare)
  • Fluorescence Microscopy of Nanochannel-Confined DNA
  • 2024
  • Ingår i: Methods in Molecular Biology. - 1940-6029 .- 1064-3745. - 9781071633762 - 9781071633779 ; , s. 175-202
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
    • Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.
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33.
  • Levin, Sune, 1991, et al. (författare)
  • A nanofluidic device for parallel single nanoparticle catalysis in solution
  • 2019
  • Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 10:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Studying single catalyst nanoparticles, during reaction, eliminates averaging effects that are an inherent limitation of ensemble experiments. It enables establishing structure-function correlations beyond averaged properties by including particle-specific descriptors such as defects, chemical heterogeneity and microstructure. Driven by these prospects, several single particle catalysis concepts have been implemented. However, they all have limitations such as low throughput, or that they require very low reactant concentrations and/or reaction rates. In response, we present a nanofluidic device for highly parallelized single nanoparticle catalysis in solution, based on fluorescence microscopy. Our device enables parallel scrutiny of tens of single nanoparticles, each isolated inside its own nanofluidic channel, and at tunable reaction conditions, ranging from the fully mass transport limited regime to the surface reaction limited regime. In a wider perspective, our concept provides a versatile platform for highly parallelized single particle catalysis in solution and constitutes a promising application area for nanofluidics.
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34.
  • Levin, Sune, 1991, et al. (författare)
  • Nanofluidic Trapping of Faceted Colloidal Nanocrystals for Parallel Single-Particle Catalysis
  • 2022
  • Ingår i: Acs Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 16:9
  • Tidskriftsartikel (refereegranskat)abstract
    • Catalyst activity can depend distinctly on nano -particle size and shape. Therefore, understanding the structure sensitivity of catalytic reactions is of fundamental and technical importance. Experiments with single-particle resolution, where ensemble-averaging is eliminated, are required to study it. Here, we implement the selective trapping of individual spherical, cubic, and octahedral colloidal Au nanocrystals in 100 parallel nanofluidic channels to determine their activity for fluorescein reduction by sodium borohydride using fluorescence microscopy. As the main result, we identify distinct structure sensitivity of the rate-limiting borohydride oxidation step originating from different edge site abundance on the three particle types, as confirmed by first -principles calculations. This advertises nanofluidic reactors for the study of structure-function correlations in catalysis and identifies nanoparticle shape as a key factor in borohydride-mediated catalytic reactions.
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35.
  • Lin, Jun, et al. (författare)
  • Bandpass filtering of DNA elastic modes using confinement and tension
  • 2012
  • Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 102, s. 96-100
  • Tidskriftsartikel (refereegranskat)abstract
    • During a variety of biological and technological processes, biopolymers are simultaneously subject to both confinement and external forces. Although significant efforts have gone into understanding the physics of polymers that are only confined, or only under tension, little work has been done to explore the effects of the interplay of force and confinement. Here, we study the combined effects of stretching and confinement on a polymer's configurational freedom. We measure the elastic response of long double-stranded DNA molecules that are partially confined to thin, nanofabricated slits. We account for the data through a model in which the DNA's short-wavelength transverse elastic modes are cut off by applied force and the DNA's bending stiffness, whereas long-wavelength modes are cut off by confinement. Thus, we show that confinement and stretching combine to permit tunable bandpass filtering of the elastic modes of long polymers. © 2012 Biophysical Society.
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36.
  • McGinn, Steven, et al. (författare)
  • New Technologies for DNA analysis-A review of the READNA Project.
  • 2016
  • Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
  • Forskningsöversikt (refereegranskat)abstract
    • The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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37.
  • Motta, M., et al. (författare)
  • Controllable morphology of flux avalanches in microstructured superconductors
  • 2014
  • Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 89:13
  • Tidskriftsartikel (refereegranskat)abstract
    • The morphology of abrupt bursts of magnetic flux into superconducting films with engineered periodic pinning centers (antidots) has been investigated. Guided flux avalanches of thermomagnetic origin develop a treelike structure, with the main trunk perpendicular to the borders of the sample, while secondary branches follow well-defined directions determined by the geometrical details of the underlying periodic pinning landscape. Strikingly, we demonstrate that in a superconductor with relatively weak random pinning the morphology of such flux avalanches can be fully controlled by proper combinations of lattice symmetry and antidot geometry. Moreover, the resulting flux patterns can be reproduced, to the finest details, by simulations based on a phenomenological thermomagnetic model. In turn, this model can be used to predict such complex structures and to estimate physical variables of more difficult experimental access, such as the local values of temperature and electric field.
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38.
  • Motta, M., et al. (författare)
  • Enhanced pinning in superconducting thin films with graded pinning landscapes
  • 2013
  • Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 102:21
  • Tidskriftsartikel (refereegranskat)abstract
    • A graded distribution of antidots in superconducting a-Mo79Ge21 thin films has been investigated by magnetization and magneto-optical imaging measurements. The pinning landscape has maximum density at the sample border, decreasing linearly towards the center. Its overall performance is noticeably superior than that for a sample with uniformly distributed antidots: For high temperatures and low fields, the critical current is enhanced, whereas the region of thermomagnetic instabilities in the field-temperature diagram is significantly suppressed. These findings confirm the relevance of graded landscapes on the enhancement of pinning efficiency, as recently predicted by Misko and Nori.
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39.
  • Müller, Vilhelm, 1990, et al. (författare)
  • Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.
  • 2016
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 6, s. 37938-
  • Tidskriftsartikel (refereegranskat)abstract
    • Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.
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40.
  • Müller, Vilhelm, 1990, et al. (författare)
  • Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping
  • 2016
  • Ingår i: Acs Infectious Diseases. - : American Chemical Society (ACS). - 2373-8227. ; 2:5, s. 322-328
  • Tidskriftsartikel (refereegranskat)abstract
    • Resistance to life-saving antibiotics increases rapidly worldwide, and multiresistant bacteria have become a global threat to human health. Presently, the most serious threat is the increasing spread of Enterobacteriaceae carrying genes coding for extended spectrum beta-lactamases (ESBL) and carbapenemases on highly mobile plasmids. We here demonstrate how optical DNA maps of single plasmids can be used as fingerprints to trace plasmids, for example, during resistance outbreaks. We use the assay to demonstrate a potential transmission route of an ESBL-carrying plasmid between bacterial strains/species and between patients, during a polyclonal outbreak at a neonatal ward at Sahlgrenska University Hospital (Gothenburg, Sweden). Our results demonstrate that optical DNA mapping is an easy and rapid method for detecting the spread of plasmids mediating resistance. With the increasing prevalence of multiresistant bacteria, diagnostic tools that can aid in solving ongoing routes of transmission, in particular in hospital settings, will be of paramount importance.
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