Mechanofluorescent Polymer Brush Surfaces that Spatially Resolve Surface Solvation.

Polymer brushes, consisting of densely end-tethered polymers to a surface, can exhibit rapid and sharp conformational transitions due to specific stimuli, which offer intriguing possibilities for surface-based sensing of the stimuli. The key toward unlocking these possibilities is the development of methods to readily transduce signals from polymer conformational changes. Herein, we report on single-fluorophore integrated ultrathin (<40 nm) polymer brush surfaces that exhibit changing fluorescence properties based on polymer conformation. The basis of our methods is the change in occupied volume as the polymer brush undergoes a collapse transition, which enhances the effective concentration and aggregation of the integrated fluorophores, leading to a self-quenching of the fluorophores' fluorescence and thereby reduced fluorescence lifetimes. By using fluorescence lifetime imaging microscopy, we reveal spatial details on polymer brush conformational transitions across complex interfaces, including at the air-water-solid interface and at the interface of immiscible liquids that solvate the surface. Furthermore, our method identifies the swelling of polymer brushes from outside of a direct droplet (i.e., the polymer phase with vapor above), which is controlled by humidity. These solvation-sensitive surfaces offer a strong potential for surface-based sensing of stimuli-induced phase transitions of polymer brushes with spatially resolved output in high resolution.

Transcription Factor Binding Affinities and DNA Shape Readout.

An essential event in gene regulation is the binding of a transcription factor (TF) to its target DNA. Models considering the interactions between the TF and the DNA geometry proved to be successful approaches to describe this binding event, while conserving data interpretability. However, a direct characterization of the DNA shape contribution to binding is still missing due to the lack of accurate and large-scale binding affinity data. Here, we use a binding assay we recently established to measure with high sensitivity the binding specificities of 13 Drosophila TFs, including dinucleotide dependencies to capture non-independent amino acid-base interactions. Correlating the binding affinities with all DNA shape features, we find that shape readout is widely used by these factors. A shape readout/TF-DNA complex structure analysis validates our approach while providing biological insights such as positively charged or highly polar amino acids often contact nucleotides that exhibit strong shape readout.

Sensitive Automated Measurement of Histone-DNA Affinities in Nucleosomes.

The DNA of eukaryotes is wrapped around histone octamers to form nucleosomes. Although it is well established that the DNA sequence significantly influences nucleosome formation, its precise contribution has remained controversial, partially owing to the lack of quantitative affinity data. Here, we present a method to measure DNA-histone binding free energies at medium throughput and with high sensitivity. Competitive nucleosome formation is achieved through automation, and a modified epifluorescence microscope is used to rapidly and accurately measure the fractions of bound/unbound DNA based on fluorescence anisotropy. The procedure allows us to obtain full titration curves with high reproducibility. We applied this technique to measure the histone-DNA affinities for 47 DNA sequences and analyzed how the affinities correlate with relevant DNA sequence features. We found that the GC content has a significant impact on nucleosome-forming preferences, but 10 bp dinucleotide periodicities and the presence of poly(dA:dT) stretches do not.

SERS and plasmonic heating efficiency from anisotropic core/satellite superstructures.

The optical properties of nanoparticle assemblies can be tailored via hybridization of plasmon modes. Isotropic core/satellite superstructures made of spherical nanoparticles are known to exhibit coupled modes with a strongly scattering (radiative) character, and provide hot spots yielding high activity in surface-enhanced Raman scattering (SERS). However, to complement this functionality with plasmonic heating, additional absorbing (non-radiative) modes are required. We introduce herein anisotropic superstructures formed by decorating a central nanorod with spherical satellite nanoparticles, which feature two coupled modes that allow application for both SERS and heating. On the basis of diffuse reflectance spectroscopy, small-angle X-ray scattering (SAXS), and electromagnetic simulations, the origin of the coupled modes is disclosed and thus serves as a basis toward alternative designs of functional superstructures. This work represents a proof-of-principle for the combination of high SERS efficiency with efficient plasmonic heating by near-infrared irradiation.

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy.

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing approaches suffer from significant limitations, we have developed a new method for determining TF-DNA binding affinities with high sensitivity on a large scale. The assay relies on the established fluorescence anisotropy (FA) principle but introduces important technical improvements. First, we measure a full FA competitive titration curve in a single well by incorporating TF and a fluorescently labeled reference DNA in a porous agarose gel matrix. Unlabeled DNA oligomer is loaded on the top as a competitor and, through diffusion, forms a spatio-temporal gradient. The resulting FA gradient is then read out using a customized epifluorescence microscope setup. This improved setup greatly increases the sensitivity of FA signal detection, allowing both weak and strong binding to be reliably quantified, even for molecules of similar molecular weights. In this fashion, we can measure one titration curve per well of a multi-well plate, and through a fitting procedure, we can extract both the absolute dissociation constant (KD) and active protein concentration. By testing all single-point mutation variants of a given consensus binding sequence, we can survey the entire binding specificity landscape of a TF, typically on a single plate. The resulting position weight matrices (PWMs) outperform those derived from other methods in predicting in vivo TF occupancy. Here, we present a detailed guide for implementing HiP-FA on a conventional automated fluorescent microscope and the data analysis pipeline.

Author Correction: True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy.

In the original version of this Article, equation three contained a sign error whereby the term RT was added when it should have been subtracted. This has now been corrected in the PDF and HTML versions of the Article.

True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy.

The complex patterns of gene expression in metazoans are controlled by selective binding of transcription factors (TFs) to regulatory DNA. To improve the quantitative understanding of this process, we have developed a novel method that uses fluorescence anisotropy measurements in a controlled delivery system to determine TF-DNA binding energies in solution with high sensitivity and throughput. Owing to its large dynamic range, the method, named high performance fluorescence anisotropy (HiP-FA), allows for reliable quantification of both weak and strong binding; binding specificities are calculated on the basis of equilibrium constant measurements for mutational DNA variants. We determine the binding preference landscapes for 26 TFs and measure high absolute affinities, but mostly lower binding specificities than reported by other methods. The revised binding preferences give rise to improved predictions of in vivo TF occupancy and enhancer expression. Our approach provides a powerful new tool for the systems-biological analysis of gene regulation.

Nanorattles with tailored electric field enhancement.

Nanorattles are metallic core-shell particles with core and shell separated by a dielectric spacer. These nanorattles have been identified as a promising class of nanoparticles, due to their extraordinary high electric-field enhancement inside the cavity. Limiting factors are reproducibility and loss of axial symmetry owing to the movable metal core; movement of the core results in fluctuation of the nanocavity dimensions and commensurate variations in enhancement factor. We present a novel synthetic approach for the robust fixation of the central gold rod within a well-defined box, which results in an axisymmetric nanorattle. We determine the structure of the resulting axisymmetric nanorattles by advanced transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS). Optical absorption and scattering cross-sections obtained from UV-vis-NIR spectroscopy quantitatively agree with finite-difference time-domain (FDTD) simulations based on the structural model derived from SAXS. The predictions of high and homogenous field enhancement are evidenced by scanning TEM electron energy loss spectroscopy (STEM-EELS) measurement on single-particle level. Thus, comprehensive understanding of structural and optical properties is achieved for this class of nanoparticles, paving the way for photonic applications where a defined and robust unit cell is crucial.

Template-assisted colloidal self-assembly of macroscopic magnetic metasurfaces.

We demonstrate a template-assisted colloidal self-assembly approach for magnetic metasurfaces on macroscopic areas. The choice of anisotropic colloidal particle geometry, assembly pattern and metallic film is based on rational design criteria, taking advantage of mirror-charge effects for gold nanorods placed on gold film. Monodisperse gold nanorods prepared utilizing wet-chemistry are arranged with high precision on wrinkled templates to form linear array-type assemblies and subsequently transferred to a thin gold film. Due to the obtained particle-to-film distance of 1.1 nm, the plasmonic mode of the nanorod is able to couple efficiently with the supporting metallic film, giving rise to a magnetic mode in the visible spectrum (721 nm). Conventional UV-vis-NIR measurements in close correlation with electromagnetic simulations provide evidence for the presence of a magnetic resonance on the macroscopic area. The herein presented scalable lithography-free fabrication process paves the road towards colloidal functional metasurfaces with an optical response in the effective magnetic permeability.

Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron-limited conditions.

Microorganisms can be versatile in their interactions with each other, being variously beneficial, neutral or antagonistic in their effect. Although this versatility has been observed among many microorganisms and in many environments, little is known regarding the mechanisms leading to these changes in behavior. In the present work, we analyzed the mechanism by which the soil bacterium Pseudomonas fluorescens BBc6R8 shifts from stimulating the growth of the ectomycorrhizal fungus Laccaria bicolor S238N to killing the fungus. We show that among the three secondary metabolites produced by the bacterial strain-the siderophores enantio-pyochelin and pyoverdine, and the biosurfactant viscosin-the siderophores are mainly responsible for the antagonistic activity of the bacterium under iron-limited conditions. While the bacterial strain continues to produce beneficial factors, their effects are overridden by the action of their siderophores. This antagonistic activity of the strain P. fluorescens BBC6R8 in iron-depleted environments is not restricted to its influence on L. bicolor, since it was also seen to inhibit the growth of the actinomycete Streptomyces ambofaciens ATCC23877. We show that the strain P. fluorescens BBc6R8 uses different strategies to acquire iron, depending on certain biotic and abiotic factors.