| 1. |
- Fritzsche, Joachim, 1977, et al.
(författare)
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Single Particle Nanoplasmonic Sensing in Individual Nanofluidic Channels
- 2016
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 16:12, s. 7857-7864
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Tidskriftsartikel (refereegranskat)abstract
- Nanoplasmonics allows label-free optical sensing and spectroscopy at the single nanoparticle level by exploiting plasmonic excitations in metal nanoparticles. Nanofluidics offers exclusive possibilities for applying and controlling fluid flow and mass transport at the nanoscale and toward nanosized objects. Here, we combine these two concepts in a single device, by integrating single particle nanoplasmonic sensing with nanofluidics using advanced nanofabrication. The developed devices enable on-chip referenced parallel single particle nanoplasmonic sensing inside multiple individual nanofluidic channels with dimensions down to the 100 nm range. Beyond detailed discussion of the nanofabrication, general device characterization, and parallelized single particle plasmonic readout concepts, we demonstrate device function on two examples: (i) in situ measurements of local buffer concentrations inside a nanofluidic channel; (ii) real time binding kinetics of alkanethiol molecules to a single plasmonic nanonatenna sensor in a single nanochannel. Our concept thus provides a powerful solution for controlling mass transport to and from individual (plasmonic) nanoparticles, which in a long-term perspective offers unique opportunities for label-free detection of analyte molecules at low concentrations and for fundamental studies of fluids in extreme confinement.
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| 2. |
- Albinsson, David, 1990, et al.
(författare)
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Single Particle Nanoplasmonic Sensing in Individual Nanofluidic Channels
- 2017
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Ingår i: The 8th International Conference on Surface Plasmon Photonics (SPP8).
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Konferensbidrag (refereegranskat)abstract
- By combining the precise mass transport control of nanofluidics with the single particle sensing abilities of nanoplasmonics we demonstrate real time single particle parallel readout of multiple nanofluidic channels from the same chip using plasmonic nanospectroscopy.The exceptional label-free sensitivity of individual plasmonic nanoparticles combined with dark-field scattering spectroscopy has proven to be a powerful tool in catalysis[1], materials science[2], and gas sensing[3], as well as to detect single molecular binding events[4]. However, despite the proven sensitivity of single particle plasmonic nanosensors, the detection of ultralow concentrations of specific analyte molecules is limited by the fact that they usually are free to diffuse away from the sensing surface, which gives rise to unpractical detection times on the order of days.As a first step to alleviate this limitation, we present an integrated nanoplasmonic-nanofluidic platform comprised of nanochannels integrated with a single plasmonic nanoantenna sensor, schematically presented in Fig 1. The dimensions of the nanofluidic system are chosen such that the entire volume of analyte solution is forced to pass the plasmonic sensor within the decay length of the near field, in order to significantly enhance the probability of direct interaction of the sensor surface with analyte in the channel. The developed devices enable on-chip referenced parallel single particle nanoplasmonic sensing inside multiple individual nanofluidic channels with dimensions down to the 100 nm range. Beyond detailed discussion of the nanofabrication, general device characterization, and parallelized single particle plasmonic readout concepts, we present the device function on two examples: (i) in situ measurements of local buffer concentrations inside a nanofluidic channel; (ii) real time binding kinetics of alkanethiol molecules to a single plasmonic nanoantenna sensor in a single nanochannel.
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| 3. |
- 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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| 4. |
- 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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| 5. |
- Brisbois, J., et al.
(författare)
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Flux penetration in a superconducting film partially capped with a conducting layer
- 2017
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Ingår i: Physical Review B. - 2469-9969 .- 2469-9950. ; 95:9
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Tidskriftsartikel (refereegranskat)abstract
- The influence of a conducting layer on the magnetic flux penetration in a superconducting Nb film is studied by magneto-optical imaging. The metallic layer partially covering the superconductor provides an additional velocity-dependent damping mechanism for the flux motion that helps to protect the superconducting state when thermomagnetic instabilities develop. If the flux advances with a velocity slower than omega = 2/mu(0)sigma t, where sigma is the cap layer conductivity and t is its thickness, the flux penetration remains unaffected, whereas for incoming flux moving faster than w, the metallic layer becomes an active screening shield. When the metallic layer is replaced by a perfect conductor, it is expected that the flux braking effect will occur for all flux velocities. We investigate this effect by studying Nb samples with a thickness step. Some of the observed features, namely the deflection of the flux trajectories at the border of the thick center, as well as the favored flux penetration at the indentation, are reproduced by time-dependent Ginzburg-Landau simulations.
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| 6. |
- Fornander, Louise, 1984, et al.
(författare)
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Using nanofluidic channels to probe dynamics of RAD51-Filaments
- 2015
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Ingår i: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1826-1828
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Konferensbidrag (refereegranskat)abstract
- Using nanochannels, passivated with a lipid bilayer to avoid sticking of proteins, we study Rad51 filaments bound to single- and double stranded DNA. We demonstrate how we can discern different properties of the filaments by studying them at different degrees of confinement. Unlike the bacterial homologue RecA, that forms homogeneous filaments along DNA, Rad51 forms heterogeneous filaments containing both rigid kinks as well as flexible regions. Varying the counterion, the DNA substrate as well as the initial protein concentration, we try to understand the factors governing the structure of the filaments.
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| 7. |
- Fornander, Louise, 1984, et al.
(författare)
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Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels
- 2016
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 32:33, s. 8403-8412
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Tidskriftsartikel (refereegranskat)abstract
- RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg2+ or Ca2+), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
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| 8. |
- Freitag, C., et al.
(författare)
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Visualizing the entire DNA from a chromosome in a single frame
- 2015
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Ingår i: Biomicrofluidics. - : AIP Publishing. - 1932-1058. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.
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| 9. |
- Friedrich, R., et al.
(författare)
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A nano flow cytometer for single lipid vesicle analysis
- 2017
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Ingår i: Lab on a Chip - Miniaturisation for Chemistry and Biology. - : Royal Society of Chemistry (RSC). - 1473-0189 .- 1473-0197. ; 17:5, s. 830-841
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Tidskriftsartikel (refereegranskat)abstract
- We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 mu l sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.
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| 10. |
- Frykholm, Karolin, 1977, et al.
(författare)
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Fast size-determination of intact bacterial plasmids using nanofluidic channels
- 2015
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Ingår i: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0189 .- 1473-0197. ; 15:13, s. 2739-2743
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate how nanofluidic channels can be used as a tool to rapidly determine the number and sizes of plasmids in bacterial isolates. Each step can be automated at low cost, opening up opportunities for general use in microbiology labs.
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