| 11. |
- Singh, Vandana, 1985, et al.
(författare)
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Shining light on single-strand lesions caused by the chemotherapy drug bleomycin
- 2021
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Ingår i: DNA Repair. - : Elsevier BV. - 1568-7864 .- 1568-7856. ; 105
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Tidskriftsartikel (refereegranskat)abstract
- Quantification of the DNA damage induced by chemotherapy in patient cells may aid in personalization of the dose used. However, assays to evaluate individual patient response to chemotherapy are not available today. Here, we present an assay that quantifies single-stranded lesions caused by the chemotherapeutic drug Bleomycin (BLM) in peripheral blood mononuclear cells (PBMCs) isolated from healthy individuals. We use base excision repair (BER) enzymes to process the DNA damage induced by BLM and then extend the processed sites with fluorescent nucleotides using a DNA polymerase. The fluorescent patches are quantified on single DNA molecules using fluorescence microscopy. Using the assay, we observe a significant variation in the in vitro induced BLM damage and its repair for different individuals. Treatment of the cells with the BER inhibitor CRT0044876 leads to a lower level of repair of BLM-induced damage, indicating the ability of the assay to detect a compromised DNA repair in patients. Overall, the data suggest that our assay could be used to sensitively detect the variation in BLM-induced DNA damage and repair in patients and can potentially be able to aid in personalizing patient doses.
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| 12. |
- Spackova, Barbora, 1979, et al.
(författare)
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Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles
- 2022
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 19, s. 751-758
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Tidskriftsartikel (refereegranskat)abstract
- Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel. Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes.
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| 13. |
- Sun, Lanlan, 1981, et al.
(författare)
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Single-molecule electronics: from chemical design to functional devices
- 2014
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Ingår i: Chemical Society Reviews. - 1460-4744 .- 0306-0012. ; 43:21, s. 7378-7411
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Forskningsöversikt (refereegranskat)abstract
- The use of single molecules in electronics represents the next limit of miniaturisation of electronic devices, which would enable us to continue the trend of aggressive downscaling of silicon-based electronic devices. More significantly, the fabrication, understanding and control of fully functional circuits at the single-molecule level could also open up the possibility of using molecules as devices with novel, not-foreseen functionalities beyond complementary metal-oxide semiconductor technology (CMOS). This review aims at highlighting the chemical design and synthesis of single molecule devices as well as their electrical and structural characterization, including a historical overview and the developments during the last 5 years. We discuss experimental techniques for fabrication of single-molecule junctions, the potential application of single-molecule junctions as molecular switches, and general physical phenomena in single-molecule electronic devices.
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| 14. |
- Wranne, Moa, 1986, et al.
(författare)
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Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden
- 2024
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Ingår i: Scientific Reports. - 2045-2322 .- 2045-2322. ; 14:1, s. 11880-
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Tidskriftsartikel (refereegranskat)abstract
- Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.
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| 15. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
- 2015
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
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Tidskriftsartikel (refereegranskat)abstract
- Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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| 16. |
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| 17. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Unfolding of nanoconfined circular DNA
- 2015
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Ingår i: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 18. |
- Altenburger, Björn, 1990, et al.
(författare)
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Label-Free Imaging of Catalytic H 2 O 2 Decomposition on Single Colloidal Pt Nanoparticles Using Nanofluidic Scattering Microscopy
- 2023
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Ingår i: ACS Nano. - 1936-086X .- 1936-0851. ; 17:21, s. 21030-21043
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Tidskriftsartikel (refereegranskat)abstract
- Single-particle catalysis aims at determining factors that dictate the nanoparticle activity and selectivity. Existing methods often use fluorescent model reactions at low reactant concentrations, operate at low pressures, or rely on plasmonic enhancement effects. Hence, methods to measure single-nanoparticle activity under technically relevant conditions and without fluorescence or other enhancement mechanisms are still lacking. Here, we introduce nanofluidic scattering microscopy of catalytic reactions on single colloidal nanoparticles trapped inside nanofluidic channels to fill this gap. By detecting minuscule refractive index changes in a liquid flushed trough a nanochannel, we demonstrate that local H2O2 concentration changes in water can be accurately measured. Applying this principle, we analyze the H2O2 concentration profiles adjacent to single colloidal Pt nanoparticles during catalytic H2O2 decomposition into O2 and H2O and derive the particles’ individual turnover frequencies from the growth rate of the O2 gas bubbles formed in their respective nanochannel during reaction.
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| 19. |
- Bäcklund, Fredrik, et al.
(författare)
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Amyloid fibrils as dispersing agents for oligothiophenes: control of photophysical properties through nanoscale templating and flow induced fibril alignment
- 2014
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Ingår i: Journal of Materials Chemistry. - : Royal Society of Chemistry (RSC). - 1364-5501 .- 0959-9428 .- 2050-7526 .- 2050-7534. ; 2:37, s. 7811-7822
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Tidskriftsartikel (refereegranskat)abstract
- Herein we report that protein fibrils formed from aggregated proteins, so called amyloid fibrils, serve as an excellent dispersing agent for hydrophobic oligothiophenes such as alpha-sexithiophene (6T). Furthermore, the protein fibrils are capable of orienting 6T along the fibril long axis, as demonstrated by flow-aligned linear dichroism spectroscopy and polarized fluorescence microscopy. The materials are prepared by solid state mixing of 6T with a protein capable of self-assembly. This results in a water soluble composite material that upon heating in aqueous acid undergoes self-assembly into protein fibrils non-covalently functionalized with 6T, with a typical diameter of 5-10 nm and lengths in the micrometre range. The resulting aqueous fibril dispersions are a readily available source of oligothiophenes that can be processed from aqueous solvent, and we demonstrate the fabrication of macroscopic structures consisting of aligned 6T functionalized protein fibrils. Due to the fibril induced ordering of 6T these structures exhibit polarized light emission.
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| 20. |
- Dvirnas, Albertas, et al.
(författare)
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Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach
- 2021
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16:11
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention. In this work, we introduce HMMSV, a hidden Markov model (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach using simulated data-sets with 5 different types of SVs, and combinations thereof, and demonstrate that the method reaches a true positive rate greater than 80% for randomly generated barcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV further leads to larger true positive rates. For a real data-set with experimental barcodes on bacterial plasmids, we successfully detect matching barcode pairs and SVs without any particular assumption of the types of SVs present. Instead, our method effectively goes through all possible combinations of SVs. Since ODM works on length scales typically not reachable with other techniques, our methodology is a promising tool for identifying arbitrary combinations of genomic alterations.
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