Oriented soft dna curtains for single-molecule interaction studies.

Single-molecule techniques, which are designed for protein-DNA interaction studies, allow to gather valuable information about every individual molecule that is present in the sample. Employment of classical biochemical methods, which are based on ensemble measurements, prevents the obtainment of this useful information that is typically covered under the overall average of contribution coming from all molecules. However, vast majority of such single-molecule techniques faces with the problem of low throughput because of their incapability to manipulate more than one investigatory biomolecule at a time. Due to its principle of effective functionality “DNA Curtains” technology, which is meant for protein and DNA interaction studies at a single molecule level, effectively treats the aforementioned problem and grants a possibility to collect a large amount of statistical data during a single experiment. Recently, we have developed a platform of soft “DNA Curtains” that is based on the alternative strategy of immobilization of DNA molecules on the surface. In comparison with the other variants of traditional “DNA Curtains” tool, our experimental platform not only retains high throughput, the main attribute of this technology, but it also has some other important advantages such as low cost, simplicity and technological accessibility. Nevertheless, an efficient practical applicability of our soft “DNA Curtains” is limited by three major drawbacks – insufficient optimization of factors that influence the quality of surface-printed protein lines the most, relatively short duration of immobilization of surface-fixed individual DNA molecules and undefined orientation of biotinylated DNA molecules that are double tethered on the surface. In this work, we improved our technology of soft “DNA Curtains”. By optimizing the printing pressure, which acts during the stage of protein lift-off microcontact printing, employing traptavidin for nanopatterning of chemically modified glass surface and functionalizing the ends of DNA molecules with labels of distinct specifity – biotin and digoxigenin, respectively – we developed longer duration of immobilization of surface-fixed DNA molecules-predetermining and defined orientation of immobilized DNA molecules-ensuring version of our platform – oriented soft “DNA Curtains”. Ultimately, by employing Cas9 endonuclease, we demonstrated that this experimental tool can be successfully implemented in single protein-DNA interaction studies

DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level

Protein-DNA interactions are the core of the cell’s molecular machinery. For a long time, conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Currently single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details. In comparison to the traditional ones, SM methods allow direct monitoring of individual biomolecules. Therefore, SM methods reveal reactions that are otherwise hidden by the ensemble averaging observed in conventional bulk-type methods. SM biophysical techniques employing various nanobiotechnology methods for immobilization of studied molecules grant the possibility to monitor individual reaction trajectories of biomolecules. Next-generation in vitro SM biophysics approaches enabling high-throughput studies are characterized by much greater complexity than the ones developed previously. Currently, several high-throughput DNA flow-stretch assays have been published and have shown many benefits for mechanistic target search studies of various DNA-binding proteins, such as CRISPR-Cas, Argonaute, various ATP-fueled helicases and translocases, and others. This review focuses on SM techniques employing surface-immobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms

DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level

Protein-DNA interactions are the core of the cell’s molecular machinery. For a long time, conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Currently single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details. In comparison to the traditional ones, SM methods allow direct monitoring of individual biomolecules. Therefore, SM methods reveal reactions that are otherwise hidden by the ensemble averaging observed in conventional bulk-type methods. SM biophysical techniques employing various nanobiotechnology methods for immobilization of studied molecules grant the possibility to monitor individual reaction trajectories of biomolecules. Next-generation in vitro SM biophysics approaches enabling high-throughput studies are characterized by much greater complexity than the ones developed previously. Currently, several high-throughput DNA flow-stretch assays have been published and have shown many benefits for mechanistic target search studies of various DNA-binding proteins, such as CRISPR-Cas, Argonaute, various ATP-fueled helicases and translocases, and others. This review focuses on SM techniques employing surface-immobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms

The miEye: bench-top super-resolution microscope with cost-effective equipment

Commercial super-resolution (SR) imaging systems require a high budget, while current more affordable open source microscopy systems lack modularity and sometimes are too complex or lack reliability. We present miEye - a cost-effective microscope designed for high-resolution wide-field fluorescence imaging. The build is constructed using a CNC milled aluminum microscope body and commercially available optomechanics, with open-source Python-based microscope control, data visualization, and analysis software integration. The data acquisition software works robustly with commonly used industrial-grade complementary metal oxide semiconductor (iCMOS) cameras, performs IR beam back-reflection-based automatic focus stabilization, and allows for laser control via an Arduino-based laser relay. The open-source nature of the design is aimed to facilitate adaptation by the community. The build can be constructed for a cost of roughly 50 k €. It contains SM-fiber and MM-fiber excitation paths that are easy to interchange and an adaptable emission path. Also, it ensures <5 nm/min stability of the sample on all axes, and allows achieving <30 nm lateral resolution for dSTORM and DNA-PAINT single-molecule localization microscopy (SMLM) experiments. Thus it serves as a cost-effective and adaptable addition to the open source microscopy community and potentially will allow high-quality SR imaging even for limited-budget research groups

Formation of calprotectin inhibits amyloid aggregation of S100A8 and S100A9 proteins /

Calcium-binding S100A8 and S100A9 proteins play a significant role in various disorders due to their pro-inflammatory functions. Substantially, they are also relevant in neurodegenerative disorders via the delivery of signals for the immune response. However, at the same time, they can aggregate and accelerate the progression of diseases. Natively, S100A8 and S100A9 exist as homo- and heterodimers, but upon aggregation, they form amyloid-like oligomers, fibrils, or amorphous aggregates. In this study, we aimed to elucidate the aggregation propensities of S100A8, S100A9, and their heterodimer calprotectin by investigating aggregation kinetics, secondary structures, and morphologies of the aggregates. For the first time, we followed the in vitro aggregation of S100A8, which formed spherical aggregates, unlike the fibrillar structures of S100A9 under the same conditions. The aggregates were sensitive to amyloid-specific ThT and ThS dyes and had a secondary structure composed of β-sheets. Similarly to S100A9, S100A8 protein was stabilized by calcium ions, resulting in aggregation inhibition. Finally, the formation of S100A8 and S100A9 heterodimers stabilized the proteins in the absence of calcium ions and prevented their aggregation

Disarming of type I-F CRISPR-Cas surveillance complex by anti-CRISPR proteins AcrIF6 and AcrIF9

CRISPR-Cas systems are prokaryotic adaptive immune systems that protect against phages and other invading nucleic acids. The evolutionary arms race between prokaryotes and phages gave rise to phage anti-CRISPR (Acr) proteins that act as a counter defence against CRISPR-Cas systems by inhibiting the effector complex. Here, we used a combination of bulk biochemical experiments, X-ray crystallography and single-molecule techniques to explore the inhibitory activity of AcrIF6 and AcrIF9 proteins against the type I-F CRISPR-Cas system from Aggregatibacter actinomycetemcomitans (Aa). We showed that AcrIF6 and AcrIF9 proteins hinder Aa-Cascade complex binding to target DNA. We solved a crystal structure of Aa1-AcrIF9 protein, which differ from other known AcrIF9 proteins by an additional structurally important loop presumably involved in the interaction with Cascade. We revealed that AcrIF9 association with Aa-Cascade promotes its binding to off-target DNA sites, which facilitates inhibition of CRISPR-Cas protection

Oriented soft DNA curtains for single-molecule imaging

Over the past 20 years, single-molecule methods have become extremely important for biophysical studies. These methods, in combination with new nanotechnological platforms, can significantly facilitate experimental design and enable faster data acquisition. A nanotechnological platform, which utilizes a flow-stretch of immobilized DNA molecules, called DNA Curtains, is one of the best examples of such combinations. Here, we employed new strategies to fabricate a flow-stretch assay of stably immobilized and oriented DNA molecules using a protein template-directed assembly. In our assay, a protein template patterned on a glass coverslip served for directional assembly of biotinylated DNA molecules. In these arrays, DNA molecules were oriented to one another and maintained extended by either single- or both-end immobilization to the protein templates. For oriented both-end DNA immobilization, we employed heterologous DNA labeling and protein template coverage with the antidigoxigenin antibody. In contrast to single-end immobilization, both-end immobilization does not require constant buffer flow for keeping DNAs in an extended configuration, allowing us to study protein–DNA interactions at more controllable reaction conditions. Additionally, we increased the immobilization stability of the biotinylated DNA molecules using protein templates fabricated from traptavidin. Finally, we demonstrated that double-tethered Soft DNA Curtains can be used in nucleic acid-interacting protein (e.g., CRISPR-Cas9) binding assay that monitors the binding location and position of individual fluorescently labeled proteins on DNA

Anodic alumina/carbon composite films: extraction and characterization of the carbon-containing component

Alumina/carbon composites are modern nanomaterials used as adsorbents, catalysts, catalyst supports, supercapacitors, and electrode materials for fuel cells. Among other methods, aluminum anodizing is fairly fast and inexpensive for producing anodic alumina/carbon composites with controllable properties. In the present study, the morphology and composition of carbon-enriched anodic alumina films were obtained during aluminum anodic oxidation in formic acid with ammonium heptamolybdate (C content is ca. 5.0 mass%) or oxalic acid (C content 3.4 mass%) additives. The anodic alumina films have a wide blue fluorescence (FL) in the 400–650 nm wavelength range with a maximum at ca. 490 nm. The FL decay is nonexponential and has an average lifetime of 1.54 and 1.59 ns for ammonium heptamolybdate and oxalic acid additives, respectively. As samples obtained in sulfuric acid (i.e. without carbon) do not possess detectable FL in the 400–650 nm wavelength range, it was concluded that carbon-containing inclusions are responsible for the FL properties of the films. The initial samples were dissolved in the hot aqueous HCl solution and then dialyzed to extract the carbon-containing component. It was shown that the solutions contain nanoparticles of amorphous carbon with a 20–25 nm diameter. Carbon nanoparticles also exhibit an excitation-dependent emission behavior at 280–450 nm excitation wavelengths with average lifetimes of 7.25–8.04 ns, depending on the composition of the initial film. Carbon nanoparticle FL is caused by the core of carbon nanoparticles (CNPs) and various emission centers on their surface, such as carbonyl, carboxyl, and hydroxyl groups. As CNPs could be exceptional candidates for detection technologies, the biocompatibility assays were performed with living COS-7 mammalian cells, showing a minimal negative impact on the living cells