| 1. |
- Wilson, J., et al.
(författare)
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Base Pair Sensitivity and Enhanced ON/OFF Ratios of DNA-Binding: Donor-Acceptor-Donor Fluorophores
- 2013
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 117:40, s. 12000-12006
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Tidskriftsartikel (refereegranskat)abstract
- The photophysical properties of two recently reported live cell compatible, DNA-binding dyes, 4,6-bis(4-(4-methylpiperazin-1-yl)phenyl)pyrimidin-2-ol, 1, and [1,3-bis[4-(4-methylpiperazin-1-yl)phenyl]-1,3-propandioato-kappa O, kappa O']difluoroboron, 2, are characterized. Both dyes are quenched in aqueous solutions, while binding to sequences containing only AT pairs enhances the emission. Binding of the dyes to sequences containing only GC pairs does not produce a significant emission enhancement, and for sequences containing both AT and GC base pairs, emission is dependent on the length of the AT pair tracts. Through emission lifetime measurements and analysis of the dye redox potentials, photoinduced electron transfer with GC pairs is implicated as a quenching mechanism. Binding of the dyes to AT-rich regions is accompanied by bathochromic shifts of 26 and 30 nm, respectively. Excitation at longer wavelengths thus increases the ON/OFF ratio of the bound probes significantly and provides improved contrast ratios in solution as well as in fluorescence microscopy of living cells.
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| 2. |
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| 3. |
- 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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| 4. |
- Frykholm, Karolin, 1977, et al.
(författare)
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Probing Physical Properties of a DNA- Protein Complex Using Nanofluidic Channels
- 2014
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Ingår i: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 10:5, s. 884-887
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Tidskriftsartikel (refereegranskat)abstract
- A method to investigate physical properties of a DNA-protein complex in solution is demonstrated. By using tapered nanochannels and lipid passivation the persistence length of a RecA filament formed on double-stranded DNA is determined to 1.15 μm, in agreement with the literature, without attaching protein or DNA to any handles or surfaces.
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| 5. |
- Frykholm, Karolin, 1977, et al.
(författare)
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Probing physical properties of DNA-protein complexes using nanofluidic channels
- 2013
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Ingår i: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. - 9781632666246 ; 2, s. 1311-1313
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Konferensbidrag (refereegranskat)abstract
- We present the use of nanofluidic channels as a tool for determining physical properties of single DNA-protein complexes. By coating the nanochannels with a lipid bilayer we avoid sticking of proteins to the channel walls. RecA is a prokaryotic protein involved in recombination and DNA repair. We study filaments of RecA, bound to both double stranded (ds) and single stranded (ss) DNA. We determine the persistence length of RecA filaments on both dsDNA and ssDNA and obtain values in agreement with the literature. Neither the DNA nor the protein has to be attached to handles or surfaces, and the technique is directly transferable to Lab-on-a-Chip technologies for high throughput measurements in solution.
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| 6. |
- Nyberg, Lena, 1979, et al.
(författare)
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A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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| 7. |
- Pitter, D. R. G., et al.
(författare)
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Turn-On, Fluorescent Nuclear Stains with Live Cell Compatibility
- 2013
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7052 .- 1523-7060. ; 15:6, s. 1330-1333
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Tidskriftsartikel (refereegranskat)abstract
- DNA-binding, green and yellow fluorescent probes with excellent brightness and high on/off ratios are reported. The probes are membrane permeable, live-cell compatible, and optimally matched to 405 nm and 514 nm laser lines, making them attractive alternatives to UV-excited and blue emissive Hoechst 33342 and DAPI nuclear stains. Their electronic structure was investigated by optical spectroscopy supported by TD-DFT calculations. DNA binding is accompanied by 27- to 75-fold emission enhancements, and linear dichroism demonstrates that one dye is a groove binder while the other intercalates into DNA.
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| 8. |
- Wigenius, Jens A., 1975-, et al.
(författare)
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Dark states in oligothiophenes : evidence from fluorescence correlation spectroscopy and dynamic light scattering
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We report studies of the conjugated pentameric oligothiophene derivative p-FTAA, which changes optical properties in aqueous buffers of varying pH and concentration. Using dynamic light scattering, luminescence spectroscopy and fluorescence correlation spectroscopy, we find evidence for the formation of large clusters of p-FTAA in aqueous environment, formation of very large non-emissive clusters, and the presence of at least two dark transient states, one presumably being a triplet state. The clustering of p-FTAA is therefore an important mechanism. This work provides an interpretation of fluorescence spectra used for the detection of misfolding proteins through interaction with p-FTAA.
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| 9. |
- Wigenius, Jens A., 1975-, et al.
(författare)
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Interactions Between a Luminescent Conjugated Oligoelectrolyte and Insulin During Early Phases of Amyloid Formation
- 2011
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Ingår i: Macromolecular Bioscience. - : Wiley. - 1616-5187 .- 1616-5195. ; 11:8, s. 1120-1127
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Tidskriftsartikel (refereegranskat)abstract
- Aggregates of misfolded proteins play an important role in diseases such as Alzheimer's. Here it is demonstrated how the anionic oligothiophene p-FTAA interacts with and influences pre-fibrillar protein assemblies during the earlier stages of in vitro fibrillation. Conjugated polythiophenes have previously been demonstrated to detect and discriminate between different types of protein aggregates and also introduce luminescent or conductive properties to these nanoscale fiber structures. Fluorescence spectroscopy, DLS, TEM and FCS are employed to follow the interplay between p-FTAA and insulin during in vitro fibrillation.
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| 10. |
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