Reversible DNA micro-patterning using the fluorous effect.
Ontology highlight
ABSTRACT:
SUBMITTER: Flynn GE
PROVIDER: S-EPMC5358500 | biostudies-literature | 2017 Mar
REPOSITORIES: biostudies-literature
Publications
Reversible DNA micro-patterning using the fluorous effect.
Flynn Gabriella E GE Withers Jamie M JM Macias Gerard G Sperling Justin R JR Henry Sarah L SL Cooper Jonathan M JM Burley Glenn A GA Clark Alasdair W AW
Chemical communications (Cambridge, England) 20170301 21
We describe a new method for the immobilisation of DNA into defined patterns with sub-micron resolution, using the fluorous effect. The method is fully reversible via a simple solvent wash, allowing the patterning, regeneration and re-patterning of surfaces with no degradation in binding efficiency following multiple removal/attachment cycles of different DNA sequences. ...[more]
Similar Datasets
Project description:In an ideal 3D topological insulator (TI), the bulk is insulating and the surface conducting due to the existence of metallic states that are localized on the surface; these are the topological surface states. Quaternary Bi-based compounds of Bi(2-x)Sb(x)Te(3-y)Se(y) with finely-tuned bulk stoichiometries are good candidates for realizing ideal 3D TI behavior due to their bulk insulating character. However, despite its insulating bulk in transport experiments, the surface region of Bi(2-x)Sb(x)Te(3-y)Se(y) crystals cleaved in ultrahigh vacuum also exhibits occupied states originating from the bulk conduction band. This is due to adsorbate-induced downward band-bending, a phenomenon known from other Bi-based 3D TIs. Here we show, using angle-resolved photoemission, how an EUV light beam of moderate flux can be used to exclude these topologically trivial states from the Fermi level of Bi1.46Sb0.54Te1.7Se1.3 single crystals, thereby re-establishing the purely topological character of the low lying electronic states of the system. We furthermore prove that this process is highly local in nature in this bulk-insulating TI, and are thus able to imprint structures in the spatial energy landscape at the surface. We illustrate this by 'writing' micron-sized letters in the Dirac point energy of the system.
| S-EPMC4635360 | biostudies-literature
Project description:The direct fabrication of microstructures, having a non-symmetrical morphology with controllable inclination, presents nowadays a challenging task. Natural examples of surfaces with inclined topographies have shown to provide anisotropic functionalities, which have attracted the interest of several researchers in the last years. This work presents a microfabrication technique for producing microstructures with a determined and controllable inclination angle using two-beam Direct Laser Interference Patterning. Polyimide foils are irradiated with a 4 ns UV (266 nm) laser source producing line-like structures with a period varying from 4.6 µm to 16.5 µm. The inclinations, retrieved by tilting the sample with respect to the optical axis of the setup, are changed from 0° to 75°, introducing a well controllable and defined inclination of the structure walls. The structuring parameters (laser fluence, number of laser pulses and interference period) as well as the inclination of the microstructures are correlated with the global tilting of the sample. As a result, a determined laser fluence and number of pulses are necessary to observe a remarkable non-symmetrical morphology of the structures. In addition, the presence of structural undercuts is reported, which opens the possibility for developing new direction-dependent properties on polymeric materials. As an example, preliminary results on light diffraction are presented, showing a similar behavior as blazed diffraction gratings.
| S-EPMC6443938 | biostudies-literature
Project description:Here, we present an approach to generate materials with programmable thermochromic transition temperatures (TTTs), based on the reversible microcrystallization of anthraquinone dyes with the assistance of blended Pluronic block copolymers. At temperatures above block copolymer critical micellization temperature (CMT), hydrophobic anthraquinone dyes, including Sudan blue II, were dispersed in copolymer micelles, whereas at lower temperature, the dyes formed microcrystals driven by dye-dye and dye-Pluronic molecular interactions. The crystallization process altered the optical properties of the dye with bathochromatic shifts detectable by eye and the thermochromic process was fully reversible. Not only could Pluronic reversibly incorporate the anthraquinone dyes into micelles at elevated temperatures, but it also modulated the crystallization process and resulting morphology of microcrystals via tuning the molecular interactions when the temperature was lowered. Crystal melting transition points (and TTTs) were in agreement with the CMTs, demonstrating that the thermochromism was dependent on block copolymer micellization. Thermochromism could be readily programmed over a broad range of temperatures by changing the CMT by using different types and concentrations of Pluronics and combinations thereof.
| S-EPMC6211563 | biostudies-literature
Project description:We report characterization of aqueous solutions of dilute Lambda phage DNA containing the redox-active surfactant (11-ferrocenylundecyl)trimethylammonium bromide (FTMA) as a function of the oxidation state of the FTMA. FTMA undergoes a reversible one-electron oxidation from a reduced state that forms micelles in aqueous solution to an oxidized state (containing the ferrocenium cation) that does not self-associate in solution. This investigation sought to test the hypothesis that FTMA can be used to achieve reversible control over the conformation of DNA-surfactant complexes in solution. Whereas DNA adopts extended coil conformations in aqueous solutions, our measurements revealed that addition of reduced FTMA (2-5 microM) to aqueous solutions of DNA (5 microM in nucleotide units) resulted in coexistence of extended coils and compact globules in solution. At higher concentrations of reduced FTMA (up to 30 microM), the DNA was present as compact globules only. In contrast, oxidized FTMA had no measurable effect on the conformation of DNA, allowing DNA to maintain an extended coil state up to a concentration of 75 microM oxidized FTMA. We further demonstrate that it is possible to chemically or electrochemically transform the oxidation state of FTMA in preformed complexes of FTMA and DNA, thus achieving in situ control over the conformations of the DNA in solution. These results provide guidance for the design of surfactant systems that permit active control of DNA-surfactant interactions.
| S-EPMC2666918 | biostudies-literature
Project description:DNA nanostructures have become an important and powerful tool for studying protein function over the last 5 years. One of the challenges, though, has been the development of universal methods for patterning protein complexes on DNA nanostructures. Herein, we present a new approach for labeling DNA nanostructures by functionalizing them with a GFP nanobody. We demonstrate the ability to precisely control protein attachment via our nanobody linker using two enzymatic model systems, namely adenylyl cyclase activity and myosin motility. Finally, we test the power of this attachment method by patterning unpurified, endogenously expressed Arp2/3 protein complex from cell lysate. By bridging DNA nanostructures with a fluorescent protein ubiquitous throughout cell and developmental biology and protein biochemistry, this approach significantly streamlines the application of DNA nanostructures as a programmable scaffold in biological studies.
| S-EPMC5079250 | biostudies-literature
Project description:A micro free flow electrophoresis (?FFE) device was used to select DNA aptamers for human immunoglobulin E (IgE). The continuous nature of ?FFE allowed 1.8 × 10(14) sequences to be introduced over a period of 30 min, a 300-fold improvement in library size over capillary electrophoresis based selections (CE-SELEX). Four rounds of selection were performed within four days. Aptamers with low nM dissociation constants for IgE were identified after a single round of ?FFE selection.
| S-EPMC3454500 | biostudies-literature
Project description:Micropatterning techniques provide direct control over the spatial organization of cells at the sub-mm scale. Regulation of these spatial parameters is important for controlling cell fate and cell function. While micropatterning has proved a powerful technique for understanding the impact of cell organization on cell behaviour, current methods for micropatterning cells require complex, specialized equipment that is not readily accessible in most biological and bioengineering laboratories. In addition, currently available methods require significant protocol optimization to ensure reliable and reproducible patterning. The inaccessibility of current methods has severely limited the widespread use of micropatterning as a tool in both biology and tissue engineering laboratories. Here we present a simple, cheap, and fast method to micropattern mammalian cells into stripes and circular patterns using Parafilm™, a common material found in most biology and bioengineering laboratories. Our method does not require any specialized equipment and does not require significant method optimization to ensure reproducible patterning. Although our method is limited to simple patterns, these geometries are sufficient for addressing a wide range of biological problems. Specifically, we demonstrate i) that using our Parafilm™ insert method we can pattern and co-pattern ARPE-19 and MDCK epithelial cells into circular and stripe micropatterns in tissue culture polystyrene (TCPS) wells and on glass slides, ii) that we can contain cells in the desired patterns for more than one month and iii) that upon removal of the Parafilm™ insert we can release the cells from the containment pattern and allow cell migration outward from the original pattern. We also demonstrate that we can exploit this confinement release feature to conduct an epithelial cell wound healing assay. This novel micropatterning method provides a reliable and accessible tool with the flexibility to address a wide range of biological and engineering problems that require control over the spatial and temporal organization of cells.
| S-EPMC3110254 | biostudies-literature
Project description:Azopolymers are known to exhibit a strong light responsivity known as athermal photofluidization. Although the underlying physics is still under debate, athermal photofluidization has been demonstrated to trigger mass-migration according to the polarization of a proper illumination light. Here, a polymer blend is proposed wherein a commercial azo-polyelectrolyte is mixed with a passive polymer. The blend is patterned as an array of micro-pillars that are individually exposed to visible laser illumination. Thanks to the interplay between the two blend components, a reversible and controlled deformation of the micro-pillars by periodically tuning the laser polarization in time is demonstrated. A reduced mobility of the azo-compound allows to repeatibly elongate and rotate micro-pillars along specific directions, with no significant material flow outisde the initial volume and no significant degradation of the structure morphology over several cycles. The proposed work suggests new degrees of freedom in controlling the mechanical features of micro-patterned light-responsive materials that can be usefully exploited in many application fields.
| S-EPMC4987756 | biostudies-literature
Project description:In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient's tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding xenografts, which were actually more similar to their original parental tumors. This points to the potentially critical role of the brain microenvironment in influencing methylation and transcriptional patterns of GSCs. Consistent with this possibility, ex vivo cultured GSCs isolated from xenografts showed a tendency to return to their initial in vitro states even after a short time in culture, supporting a rapid dynamic adaptation to the in vitro microenvironment. These results show that methylation and transcriptome profiles are highly dependent on the microenvironment and growth in orthotopic sites partially reverse the changes caused by in vitro culturing.
| S-EPMC3984100 | biostudies-literature
Project description:Improved imaging of cancerous tissue has the potential to aid prognosis and improve patient outcome through longitudinal imaging of treatment response and disease progression. While nuclear imaging has made headway in cancer imaging, fluorinated tracers that enable magnetic resonance imaging (19F MRI) hold promise, particularly for repeated imaging sessions because nonionizing radiation is used. Fluorine MRI detects molecular signatures by imaging a fluorinated tracer and takes advantage of the spatial and anatomical resolution afforded by MRI. This manuscript describes a fluorous polymeric nanoparticle that is capable of 19F MR imaging and fluorescent tracking for in vitro and in vivo monitoring of immune cells and cancerous tissue. The fluorous particle is derived from low-molecular-weight amphiphilic copolymers that self-assemble into micelles with a hydrodynamic diameter of 260 nm. The polymer is MR-active at concentrations as low as 2.1 mM in phantom imaging studies. The fluorinated particle demonstrated rapid uptake into immune cells for potential cell-tracking or delineation of the tumor microenvironment and showed negligible toxicity. Systemic administration indicates significant uptake into two tumor types, triple-negative breast cancer and ovarian cancer, with little accumulation in off-target tissue. These results indicate a robust platform imaging agent capable of immune cell tracking and systemic disease monitoring with exceptional uptake of the nanoparticle in multiple cancer models.
| S-EPMC5561414 | biostudies-literature