Oligomers In Solution Research Articles

Localization of the E. coli Dps protein molecules in a silicon wires matrix according to scanning electron microscopy and X-ray photoelectron spectroscopy

The work is related to the study of the morphological features of silicon wires arrays combined with a nanomaterial of natural origin, a bacterial ferritin-like protein Dps, and their relationship with the composition of the surface and interior. A silicon wires array was formed by metal-assisted wet chemical etching. To obtain recombinant protein, Escherichia coli BL21*(DE3) cells were used as producers, and purification was carried out by the chromatography method. The combination of silicon wires with protein molecules was carried out by layering under laboratory conditions, followed by drying. The resulting hybrid material was studied by scanning electron microscopy and X-ray photoelectron spectroscopy. The initial silicon wires array had sharp boundaries on the surface. The diameter of the silicon wires was about 100 nm, while the distances between the wires can vary widely, reaching several hundred nanometres or be less than 100 nanometres, depending on the formation conditions, in the absence of noticeable transition layers. The pores formed in this way are available for filling with protein during deposition. The effectiveness of using the scanning electron microscopy method to study the morphology of the hybrid material “silicon wires – bacterial protein Dps” as well as X-ray photoelectron spectroscopy method together with ion etching for the investigation of the composition and physico-chemical of the hybrid material was demonstrated. Complementary results have shown that the molecular culture, which is a solution of oligomers of the recombinant Dps protein of E.coli bacterial cells, can penetrate deep into the pores of the silicon wires array with an extremely developed surface. The possibility of the control of the filling of silicon wires arrays by varying the pore morphology and other modes of formation of structuresand their surface has been demonstrated. The obtained data can be used to study the possibilities of the functionalization of the developed surface of silicon wires by their driven coating with controlled delivery of biohybrid material.

SynDLP is a dynamin-like protein of Synechocystis sp. PCC 6803 with eukaryotic features

Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin-like protein of the cyanobacterium Synechocystis sp. PCC 6803, forms ordered oligomers in solution. The 3.7 Å resolution cryo-EM structure of SynDLP oligomers reveals the presence of oligomeric stalk interfaces typical for eukaryotic dynamin-like proteins. The bundle signaling element domain shows distinct features, such as an intramolecular disulfide bridge that affects the GTPase activity, or an expanded intermolecular interface with the GTPase domain. In addition to typical GD-GD contacts, such atypical GTPase domain interfaces might be a GTPase activity regulating tool in oligomerized SynDLP. Furthermore, we show that SynDLP interacts with and intercalates into membranes containing negatively charged thylakoid membrane lipids independent of nucleotides. The structural characteristics of SynDLP oligomers suggest it to be the closest known bacterial ancestor of eukaryotic dynamin.

Spontaneous Mesoporosity-Driven Sequestration of Ionic Liquids from Silicone-Based Reference Electrode Membranes

Nanopore-driven sequestration of ionic liquids from a silicone membrane is presented, a phenomenon that has not been reported previously. Reference electrodes with ionic liquid doped polydimethylsiloxane (PDMS) reference membranes and colloid-imprinted mesoporous carbon (CIM) as solid contact are not functional unless special attention is paid to the porosity of the solid contact. In the fabrication of such reference electrodes, a solution of a hydroxyl-terminated silicone oligomer, ionic liquid, cross-linking reagent, and polymerization catalyst is deposited on top of the carbon layer, rapidly filling the pores of the CIM carbon. The catalyzed polymerization curing of the silicone quickly results in cross-linking of the hydroxyl-terminated polydimethylsiloxane oligomers, forming structures that are too large to penetrate the CIM carbon pores. Therefore, as solvent evaporation from the top of freshly prepared membranes drives the diffusional transport of solvent toward that membrane surface, the solvent molecules that leave the CIM carbon pores can only be replaced by the ionic liquid. This depletes the ionic liquid in the reference membrane that overlies the CIM carbon solid contact and increases the membrane resistance by up to 3 orders of magnitude, rendering the devices dysfunctional. This problem can be avoided by presaturating the CIM carbon with ionic liquid prior to the deposition of the solution that contains the silicone oligomers and ionic liquid. Alternatively, a high amount of ionic liquid can be added into the membrane solution to account for the size-selective sequestration of ionic liquid into the carbon pores. Either way, a wide variety of ionic liquids can be used to prepare PDMS-based reference electrodes with CIM carbon as a solid contact. A similar depletion of the K+ ionophore BME-44 from ion-selective silicone membranes was observed too, highlighting that the depletion of active ingredients from polymeric ion-selective and reference membranes due to interactions with high surface area solid contacts may be a more common phenomenon that so far has been overlooked.

Insights into the oligomeric structure of the HIV-1 Vpu protein

The HIV-1-encoded protein Vpu forms an oligomeric ion channel/pore in membranes and interacts with host proteins to support the virus lifecycle. However, Vpu molecular mechanisms are currently not well understood. Here, we report on the Vpu oligomeric organization under membrane and aqueous conditions and provide insights into how the Vpu environment affects the oligomer formation. For these studies, we designed a maltose-binding protein (MBP)-Vpu chimera protein and produced it in E. coli in soluble form. We analyzed this protein using analytical size-exclusion chromatography (SEC), negative staining electron microscopy (nsEM), and electron paramagnetic resonance (EPR) spectroscopy. Surprisingly, we found that MBP-Vpu formed stable oligomers in solution, seemingly driven by Vpu transmembrane domain self-association. A coarse modeling of nsEM data as well as SEC and EPR data suggests that these oligomers most likely are pentamers, similar to what was reported regarding membrane-bound Vpu. We also noticed reduced MBP-Vpu oligomer stability upon reconstitution of the protein in β-DDM detergent and mixtures of lyso-PC/PG or DHPC/DHPG. In these cases, we observed greater oligomer heterogeneity, with MBP-Vpu oligomeric order generally lower than in solution; however, larger oligomers were also present. Notably, we found that in lyso-PC/PG, above a certain protein concentration, MBP-Vpu assembles into extended structures, which had not been reported for Vpu. Therefore, we captured various Vpu oligomeric forms, which can shed light on Vpu quaternary organization. Our findings could be useful in understanding Vpu organization and function in cellular membranes and could provide information regarding the biophysical properties of single-pass transmembrane proteins.

Single-molecule spectroscopy of Apolipoprotein E reveals a complex conformational ensemble.

The ε4-allele variant of Apolipoprotein E (ApoE4) is the strongest genetic risk factor for Alzheimer's disease, though it only differs from its neutral counterpart ApoE3 by a single amino acid substitution. While ApoE4 influences the formation of plaques and neurofibrillary tangles, the structural determinants of its pathogenicity remain undetermined due to limited structural information. Previous studies have led to conflicting models of the C-terminal region positioning with respect to the N-terminal domain across isoforms, largely due to the potential contribution of data representing heterogenous oligomers in solution. Here, we apply a combination of single-molecule spectroscopy and molecular dynamics simulations to construct an atomically-detailed model of monomeric ApoE4 and probe the effect of lipid association. Importantly, our approach overcomes previous limitations by allowing us to work at picomolar concentrations where only the monomer is present. Our data reveal that ApoE4 is far more disordered and extended than previously thought and retains significant conformational heterogeneity after binding lipids. We further investigate the impact of key mutations by inserting serine residues that mimic the ApoE3 and ApoE2 isoform sequence differences, C112S and C112S C158S, respectively. Comparing the proximity of the N- and C-terminal domains across the three major isoforms (ApoE4, ApoE3, and ApoE2) suggests that all maintain heterogenous conformations in their monomeric form, with ApoE2 adopting a slightly more compact ensemble. Inspection of local conformational changes across different domains, in the context of the full-length protein, reveals that the major difference across isoforms occurs in the conformations adopted by the C-terminal tail. Overall, these data provide a new foundation for understanding how ApoE differs from non-pathogenic and protective variants of the protein.

Structural studies of human serum albumin using cryo-EM up to 0.38 nm resolution.

Single particle cryo-electron microscopy (cryoEM) offers for large proteins the resolution close to the crystallographic resolution. Unfortunately, the current limitation for cryoEM is the molecular weight, and the smallest proteins, tested individually by the cryoEM method, rarely are less than 100 kDa in size. The aim of our research was to study the structure of human serum albumin and its oligomeric forms using a combination of cryoEM, small angle X-ray scattering (SAXS) and dynamic light scattering (DLS). HSA is a monomeric (66.4 kDa) protein, which for years has been a model system for the transport of drugs and other substances, because in the human body it binds and carries lipids or metal cations (including zinc and copper ions) as well as for basic biophysical research. Currently, over 130 HSA structures in complexes with various ligands and alone at the resolution ranging from 0.189 nm to 0.39 nm have been deposited in Protein Data Bank. Using cryoEM, we were able to obtain the HSA structure with a 0.38 nm resolution. At present, it is probably one of the smallest protein structures determined using cryoEM at near-crystallographic resolution. Using SAXS and DLS we analyzed the HSA monomer structure and its oligomers in solution and compared with the cryoEM model. This research was funded by National Science Centre (Poland), grant number 2017/27/B/ST4/00485.

Curvature sensing as an emergent property of multiscale assembly of septins

The ability of cells to sense and communicate their shape is central to many of their functions. Much is known about how cells generate complex shapes, yet how they sense and respond to geometric cues remains poorly understood. Septins are GTP-binding proteins that localize to sites of micrometer-scale membrane curvature. Assembly of septins is a multistep and multiscale process, but it is unknown how these discrete steps lead to curvature sensing. Here, we experimentally examine the time-dependent binding of septins at different curvatures and septin bulk concentrations. These experiments unexpectedly indicated that septins' curvature preference is not absolute but rather is sensitive to the combinations of membrane curvatures present in a reaction, suggesting that there is competition between different curvatures for septin binding. To understand the physical underpinning of this result, we developed a kinetic model that connects septins' self-assembly and curvature-sensing properties. Our experimental and modeling results are consistent with curvature-sensitive assembly being driven by cooperative associations of septin oligomers in solution with the bound septins. When combined, the work indicates that septin curvature sensing is an emergent property of the multistep, multiscale assembly of membrane-bound septins. As a result, curvature preference is not absolute and can be modulated by changing the physicochemical and geometric parameters involved in septin assembly, including bulk concentration, and the available membrane curvatures. While much geometry-sensitive assembly in biology is thought to be guided by intrinsic material properties of molecules, this is an important example of how curvature sensing can arise from multiscale assembly of polymers.

A lysine-based 2:1-[α/aza]-pseudopeptide series used as additives in polymeric membranes for CO2 capture: synthesis, structural studies, and application.

The current study presents for the first time the synthesis of a new 2:1-[α/aza]-pseudopeptide series possessing charged amino acids (i.e., lysine) and aims at studying the influences of chirality, backbone length, and the nature of the lysine side chains on the conformation of the 2:1-[α/aza]-oligomers in solution using NMR, FTIR spectroscopy and molecular dynamic calculations. The spectroscopic results emphasized the conservation of the β-turn conformation adopted by the trimers regardless of the chirality which demonstrated a noticeable effect on the conformation of homochiral hexamer (8c) compared with the hetero-analogue (8d). The molecular dynamic calculations predicted that the chirality and the side chain of the lysine residues caused a little distortion from the classical β-turn conformation in the case of short trimer sequences (7c and 7d), while the chirality and the backbone length exerted more distortion on the β-turn adopted by the longer hexamer sequences (8c and 8d). The large disturbance in hexamers from classical β-turn was attributed to increasing the flexibility and the possibility of molecules to adopt a more energetically favorable conformation stabilized by non-classical β-turn intramolecular hydrogen bonds. Thus, alternating d- and l-lysine amino acids in the 2:1-[α/aza]-hexamer (8d) decreases the high steric hindrance between the lysine side chains, as in the homo analogue (8c), and the distortion is less recognized. Finally, short sequences of aza-pseudopeptides containing lysine residues improve CO2 separation when used as additives in Pebax® 1074 membranes. The best membrane performances were obtained with a pseudopeptidic dimer as an additive (6b'; deprotected lysine side chain), with an increase in both ideal selectivity α CO2/N2 (from 42.8 to 47.6) and CO2 permeability (from 132 to 148 Barrer) compared to the virgin Pebax® 1074 membrane.

Accumulation and ordering of P3HT oligomers at the liquid-vapor interface with implications for thin-film morphology.

The morphology of semiconducting polymer thin films is known to have a profound effect on their opto-electronic properties. Although considerable efforts have been made to control and understand the processes which influence the structures of these systems, it remains largely unclear what physical factors determine the arrangement of polymer chains in spin-cast films. Here, we investigate the role that the liquid-vapor interfaces in chlorobenzene solutions of poly(3-hexylthiophene) [P3HT] play in the conformational geometries adopted by the polymers. Using all-atom molecular dynamics (MD), and supported by toy-model simulations, we demonstrate that, with increasing concentration, P3HT oligomers in solution exhibit a strong propensity for the liquid-vapor interface. Due to the differential solubility of the backbone and side chains of the oligomers, in the vicinity of this interface, hexyl chains and the thiophene rings, have a clear orientational preference with respect to the liquid surface. At high concentrations, we additionally establish a substantial degree of inter-oligomer alignment and thiophene ring stacking near the interface. Our results broadly concur with the limited existing experimental evidence and we suggest that the interfacial structure can act as a template for film structure. We argue that the differences in solvent affinity of the side chain and backbone moieties are the driving force for the anisotropic orientations of the polymers near the interface. This finer grained description contrasts with the usual monolithic characterization of polymer units. Since this phenomenon can be controlled by concurrent chemical design and the choice of solvents, this work establishes a fabrication principle which may be useful to develop more highly functional polymer films.

Development of diketopyrrolopyrrole-based donor-acceptor oligomers using direct arylation polymerization: Non-linear and ultrafast optical analysis, and their application in ternary organic solar cells

A series of donor-acceptor (D-A) oligomers based on thieno[3,2-b]thiophene (TT), 2,2′-bithieno[3,2-b]thiophene (BTT), and diketopyrrolopyrrole (DPP) were synthesized through eco-friendly direct arylation polymerization using two different Fagnou conditions. These DPP-based oligomers, characterized on average by the chain of 4 units, presented notable bands of infrared photoluminescence with peaks in the wavelength range 712–753 nm. Time-resolved transient absorption spectroscopy was used for a basic understanding of the dynamics of excited states in these oligomers in solution, nanoparticles, and solid films. The optical nonlinearities were also evaluated through Z-scan experiments under femtosecond excitation, finding significant cross-sections of nonlinear absorption (∼920 GM) at 950 nm. Further, these DPP-based organic materials were loaded in different weight percentages, as an electro-donor material in ternary organic solar cells in combination with poly(3-hexylthiophene) P3HT and PC71BM. An improvement in conversion efficiency of 28% regarding a binary cell was achieved with the BTT derivative due to its complementary role to recollect light in the infrared region, better energy level matching, and improved quality in the formation of solid films compared with the TT derivative, which in combination increased Jsc from 9.55 to 13.5 mA/cm2. Theoretical calculations show that oligomers of 4 units produced optimized optical properties with reduced optical band gap and maximum dipole moments.

Pressure-volume-temperature properties for binary oligomeric solutions of anisole with polyethylene glycol mono-laurate or polyethylene glycol mono-4-nonylphenyl ether at pressures up to 50MPa

Experimental of P-V-T properties are measured for two binary systems containing anisole and one of oligomeric materials (polyethylene glycol mono-laurate, PEGML, and polyethylene glycol mono-4-nonylphenyl ether, PEGNPE) at temperatures ranging from 298.15K to 348.15K and pressures up to 50 MPa. Over the whole range of experimental conditions, the excess volumes of anisole + PEGML are negative (chemical-interaction dominant) and those of anisole + PEGNPE are positive (physical-interaction dominant). The Tait equation and the Redlich-Kister type model quantitatively represents the pressure-effect on the densities and the composition-effect on the excess volumes of the investigated systems, respectively. The Flory-Orwoll-Vrij (FOV) and the Schotte equations of state with or without using one binary interaction parameter calculate the specific volumes to RMSDs no greater than 0.04% and 0.11%, respectively.

Adsorption of organic peroxides on the surface of amourphous alloys for the drugs immobilization

It was investigated wetting of surfaces of the amorphous metallic alloys (AMA) based on iron and cobalt with aqueous-ammonium solutions of oligoperoxides based on vinyl acetate, 2-tert-butylperoxy-2-methyl-5-hexen-3-yne and maleic anhydride (OP-1) and based on vinyl acetate, 3-tert-butylperoxy-3-phenylbutylmethacrylate and maleic anhydride (OP-2). The surface tension of thin films of oligoperoxideʼs aqueous-ammonia solutions was determined and were calculated values of the macromolecules adsorption. A higher surface activity of OP-2 was observed in comparison with OP-1. The values ​​of the adhesion work between contact and external metallic surfaces and solutions of oligomers were calculated.

Light-controlled friction realized by a photorheological fluid

Intelligent friction and lubrication technologies have attracted widespread interest in the fields of surface engineering, smart fluids and mechanical transmission. Here, we show reversible light-controlled friction in a photorheological fluid composed of azobenzene oligomers. The viscosity of the azobenzene oligomer solution irradiated by ultraviolet light was 19.0% higher than that irradiated with near-infrared light. The friction coefficient upon near-infrared irradiation was up to 3.62 times that under ultraviolet light. The higher friction was ascribed to the poor film forming capacity of the photosensitive rheological fluid and the higher shear resistance of the azobenzene oligomer adsorption layer upon near infrared irradiation. This light-controlled friction and viscosity could inspire more novel applications in self-adaptive liquids, photosensitive dampers, intelligent braking and fluid pipe transportation.

Elucidating the Oligomerization and Cellular Interactions of a Trimer Derived from Aβ through Fluorescence and Mass Spectrometric Studies.

Aβ oligomers play a central role in the neurodegeneration observed with Alzheimer’s disease. Our laboratory has developed covalently stabilized trimers derived from residues 17–36 of Aβ as model systems for studying Aβ oligomers. In the current study, we apply the emerging techniques of fluorescence lifetime imaging microscopy (FLIM) and native mass spectrometry (native MS) to better understand the assembly and interactions of the oligomer model system 2AT-L in aqueous solutions and with cells. 2AT-L and fluorescently labeled 2AT-L analogues assemble in the membrane-like environment of SDS-PAGE, showing diffuse bands of oligomers in equilibrium. Native ion mobility-mass spectrometry (native IM-MS) of 2AT-L allows for the identification of discrete oligomers in solution and shows similar patterns of oligomer formation between 2AT-L and fluorescently labeled analogues. Fluorescence microscopy with SH-SY5Y cells reveals that fluorescently labeled 2AT-L analogues colocalize within lysosomes. FLIM studies with phasor analysis further elucidate the assembly of 2AT-L within cells and establish the occurrence of FRET, indicating the presence of oligomers within cells. Collectively, these multiple complementary techniques help better understand the complex behavior of the 2AT-L model system.

Preparation of polyimide-metal complexes with tunable Sol-Gel transition by Introduction of Zn(II)-Coordination

Developing fully rigid-chain polyimides with reversible sol-gel/gel-sol transitions is of great interest for designing high-performance materials. To date, few approaches have been employed to construct polyimide gels other than hydrogen bonding. Here, we report a polyimide-Zn(II) complex with thermo-responsive sol-gel/gel-sol transition behavior by introducing supramolecular coordination interactions. The tunable dynamic sol-gel behaviors of polyimide-Zn(II) complexes were confirmed using rheological methods. Microstructure analysis shows that coordination interactions occur between the benzimidazole molecules and Zn(II) ions. As a result, the apparent viscosity of the polyimide-Zn(II) complex even rises approximately four orders of magnitude higher than that of the PI-neat oligomer solution. Based on the 2D-correlation spectra and X-ray diffraction results, we deduced that the formation of dense chain stacking caused by coordination effects plays an essential part in the reversible sol-gel transition. As a preliminary experiment, this work gives a novel strategy to construct polyimide gels, showing application prospects in the fabrication of porous polyimide membranes, high-performance polyimide fibers, and aerogels, etc.

MP02-11 CHARACTERIZATION OF COMPLEMENT RESISTANCE FACTOR TRAT ENCODED IN DRUG RESISTANCE PLASMIDS OF UROPATHOGENIC ESCHERICHIA COLI

You have accessJournal of UrologyCME1 May 2022MP02-11 CHARACTERIZATION OF COMPLEMENT RESISTANCE FACTOR TRAT ENCODED IN DRUG RESISTANCE PLASMIDS OF UROPATHOGENIC ESCHERICHIA COLI Chae Hee Lim, Aryana Bhati, Katelyn Lott, Jazmyn Whitfield, John Land, and Tatyana Sysoeva Chae Hee LimChae Hee Lim More articles by this author , Aryana BhatiAryana Bhati More articles by this author , Katelyn LottKatelyn Lott More articles by this author , Jazmyn WhitfieldJazmyn Whitfield More articles by this author , John LandJohn Land More articles by this author , and Tatyana SysoevaTatyana Sysoeva More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002514.11AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: The TraT protein is a multifunctional virulence factor that is encoded by conjugative F-like plasmids. A majority of multidrug-resistant uropathogenic Escherichia coli (UPEC) carry F-like plasmids and thus encode for this TraT factor. In non-pathogenic E. coli, TraT is a highly expressed outer membrane lipoprotein that protects the bacterial cell from excessive rounds of plasmid transfer, from a few bacteriophages, and from the host innate immune response via serum complement killing. Our objectives in this study were (1) to measure the protective effect of TraT in UPEC background and (2) to establish whether extracellular TraT domain is sufficient to provide serum resistance. METHODS: We used conjugation to transfer the model F’ plasmid in different E. coli backgrounds. Recombinant extracellular soluble domain TraT33-244 was purified from BL21(DE3) E. coli strain using Ni-affinity chromatography. Exponentially growing E. coli cultures with and without traT-encoding plasmids or the purified TraT domain were subjected to different doses of blood serum for 2 hours at 37°C. Viable cells were quantified as colony forming units by plating serial dilutions at 0 and 2 hours after addition of serum. RESULTS: The traT-encoding plasmid provides variable level of protection that depends on serum type, bacterial cells, time, and ratios of bacteria and serum, and can reach several orders of magnitude. We have developed a method of expression and purification of soluble TraT33-244 protein and showed that this extracellular domain forms stable oligomers in solution with five-to-six subunits. Testing this purified extracellular domain in serum resistance assays revealed that it is insufficient to exhibit the full protective action of TraT. CONCLUSIONS: In this study, we measured the protective effect of traT-encoding plasmid F’ in model E. coli strains, which displayed strong but variable serum resistance. The extracellular soluble domain of TraT protein oligomerizes, but does not strongly protect against serum killing when added to bacterial cells in trans. These results suggest that membrane localization, N-terminus, or lipidation itself are important for function of the TraT factor. Overall, this study sets the stage for further investigation into the mechanism of how TraT assists UPEC bacteria in evading innate immune responses within the host organism. Source of Funding: The University of Alabama in Huntsville startup funds to Tatyana Sysoeva © 2022 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 207Issue Supplement 5May 2022Page: e14 Advertisement Copyright & Permissions© 2022 by American Urological Association Education and Research, Inc.MetricsAuthor Information Chae Hee Lim More articles by this author Aryana Bhati More articles by this author Katelyn Lott More articles by this author Jazmyn Whitfield More articles by this author John Land More articles by this author Tatyana Sysoeva More articles by this author Expand All Advertisement PDF DownloadLoading ...

Monte Carlo molecular simulation of solution and surface-bound DNA hybridization of short oligomers at varying surface densities

DNA microarrays utilize surface bound sequences to probe for target sequences in samples of interest, and density of surface coverage plays an important role in any duplex formation and subsequent detection. Here, Monte Carlo molecular simulations utilize a modified coarse-grained DNA model to calculate the impact of binding density and arrangement as well as temperature on duplex structure and hydrogen bonding patterns for two different undecamer sequences. Results indicate a modest, sequence-dependent increase in dissociation related to the proximity of neighboring duplexes but little impact on duplex structure or hydrogen bonding pattern.

Rapid and Effective Inactivation of SARS-CoV-2 with a Cationic Conjugated Oligomer with Visible Light: Studies of Antiviral Activity in Solutions and on Supports.

This paper presents results of a study of a new cationic oligomer that contains end groups and a chromophore affording inactivation of SARS-CoV-2 by visible light irradiation in solution or as a solid coating on paper wipes and glass fiber filtration substrates. A key finding of this study is that the cationic oligomer with a central thiophene ring and imidazolium charged groups gives outstanding performance in both the killing of E. coli bacterial cells and inactivation of the virus at very short times. Our introduction of cationic N-methyl imidazolium groups enhances the light activation process for both E. coli and SARS-CoV-2 but dampens the killing of the bacteria and eliminates the inactivation of the virus in the dark. For the studies with this oligomer in solution at a concentration of 1 μg/mL and E. coli, we obtain 3 log killing of the bacteria with 10 min of irradiation with LuzChem cool white lights (mimicking indoor illumination). With the oligomer in solution at a concentration of 10 μg/mL, we observe 4 log inactivation (99.99%) in 5 min of irradiation and total inactivation after 10 min. The oligomer is quite active against E. coli on oligomer-coated paper wipes and glass fiber filter supports. The SARS-CoV-2 is also inactivated by oligomer-coated glass fiber filter papers. This study indicates that these oligomer-coated materials may be very useful as wipes and filtration materials.

Formation and stabilization mechanism of mesoscale clusters in solution.

To understand the existence of complex meso-sized solute-rich clusters, which challenge the understanding of phases and phase equilibria, the formation and stabilization mechanisms of clusters in solution during nucleation of crystals and the associated physico-chemical rules are studied in detail. An essential part of the mechanism is the formation of long-lived oligomers between solute molecules. By means of density functional theory simulation and nuclear magnetic resonance experiments, this work showed that the oligomers in solution tend to be π-π stacking dimers. Clusters are formed under the combined effect of diffusion and monomer-dimer reaction. The physically meaningful quantities such as the monomer-dimer reaction rate constants and the diffusion coefficients of both species were obtained by reaction-diffusion kinetics and diffusion-ordered spectroscopy results. The evolution of cluster radius as a function of time, and the qualitative spatial distributions of monomer and dimer densities under steady-state were plotted to better understand the formation process and the nature of the clusters.

Determining the Stoichiometry of Amyloid Oligomers by Single-Molecule Photobleaching.

Small oligomers are the initial intermediates in the pathway to amyloid fibril formation. They have a distinct identity from the monomers as well as from the protofibrils and the fibrils, both in their structure and in their properties. In many cases, they play a crucial biological role. However, due to their transient nature, they are difficult to characterize. "Oligomer" is a diffuse definition, encompassing aggregates of many different sizes, and this lack of precise definition causes much confusion and disagreement between different research groups. Here, we define the small oligomers as "n"-mers with n<10, which is the size range in which the amyloid proteins typically exist at the initial phase of the aggregation process. Since the oligomers dynamically interconvert into each other, a solution of aggregating amyloid proteins will contain a distribution of sizes. A precise characterization of an oligomeric solution will, therefore, require quantification of the relative population of each size. Size-based separation methods, such as size-exclusion chromatography, are typically used to characterize this distribution. However, if the interconversion between oligomers of different sizes is fast, this would not yield reliable results. Single-molecule photobleaching (smPB) is a direct method to evaluate this size distribution in a heterogeneous solution without separation. In addition, understanding the mechanism of action of amyloid oligomers requires knowing the affinity of each oligomer type to different cellular components, such as the cell membrane. These measurements are also amenable to smPB. Here we show how to perform smPB, both for oligomers in solution and for oligomers attached to the membrane.