Aligned macrocycle pores in ultrathin films for accurate molecular sieving.

Polymer membranes are widely used in separation processes including desalination1, organic solvent nanofiltration2,3 and crude oil fractionation4,5. Nevertheless, direct evidence of subnanometre pores and a feasible method of manipulating their size is still challenging because of the molecular fluctuations of poorly defined voids in polymers6. Macrocycles with intrinsic cavities could potentially tackle this challenge. However, unfunctionalized macrocycles with indistinguishable reactivities tend towards disordered packing in films hundreds of nanometres thick7-9, hindering cavity interconnection and formation of through-pores. Here, we synthesized selectively functionalized macrocycles with differentiated reactivities that preferentially aligned to create well-defined pores across an ultrathin nanofilm. The ordered structure was enhanced by reducing the nanofilm thickness down to several nanometres. This orientated architecture enabled direct visualization of subnanometre macrocycle pores in the nanofilm surfaces, with the size tailored to ångström precision by varying the macrocycle identity. Aligned macrocycle membranes provided twice the methanol permeance and higher selectivity compared to disordered counterparts. Used in high-value separations, exemplified here by enriching cannabidiol oil, they achieved one order of magnitude faster ethanol transport and threefold higher enrichment than commercial state-of-the-art membranes. This approach offers a feasible strategy for creating subnanometre channels in polymer membranes, and demonstrates their potential for accurate molecular separations.

Ice nucleation in aqueous solutions of short- and long-chain poly(vinyl alcohol) studied with a droplet microfluidics setup.

Poly(vinyl alcohol) (PVA) has ice binding and ice nucleating properties. Here, we explore the dependence of the molecular size of PVA on its ice nucleation activity. For this purpose, we studied ice nucleation in aqueous solutions of PVA samples with molar masses ranging from 370 to 145 000 g mol-1, with a particular focus on oligomer samples with low molar mass. The experiments employed a novel microfluidic setup that is a follow-up on the previous WeIzmann Supercooled Droplets Observation on a Microarray (WISDOM) design by Reicher et al. The modified setup introduced and characterized here, termed nanoliter Bielefeld Ice Nucleation ARraY (nanoBINARY), uses droplet microfluidics with droplets (96 ± 4) µm in diameter and a fluorinated continuous oil phase and surfactant. A comparison of homogeneous and heterogeneous ice nucleation data obtained with nanoBINARY to those obtained with WISDOM shows very good agreement, underpinning its ability to study low-temperature ice nucleators as well as homogeneous ice nucleation due to the low background of impurities. The experiments on aqueous PVA solutions revealed that the ice nucleation activity of shorter PVA chains strongly decreases with a decrease in molar mass. While the cumulative number of ice nucleating sites per mass nm of polymers with different molar masses is the same, it becomes smaller for oligomers and completely vanishes for dimer and monomer representatives such as 1,3-butanediol, propan-2-ol, and ethanol, most likely because these molecules become too small to effectively stabilize the critical ice embryo. Overall, our results are consistent with PVA polymers and oligomers acting as heterogeneous ice nucleators.

Dinuclear complex-induced DNA melting.

Dinuclear copper complexes have been designed for molecular recognition in order to selectively bind to two neighboring phosphate moieties in the backbone of double strand DNA. Associated biophysical, biochemical and cytotoxic effects on DNA were investigated in previous works, where atomic force microscopy (AFM) in ambient conditions turned out to be a particular valuable asset, since the complexes influence the macromechanical properties and configurations of the strands. To investigate and scrutinize these effects in more depth from a structural point of view, cutting-edge preparation methods and scanning force microscopy under ultra-high vacuum (UHV) conditions were employed to yield submolecular resolution images. DNA strand mechanics and interactions could be resolved on the single base pair level, including the amplified formation of melting bubbles. Even the interaction of singular complex molecules could be observed. To better assess the results, the appearance of treated DNA is also compared to the behavior of untreated DNA in UHV on different substrates. Finally, we present data from a statistical simulation reasoning about the nanomechanics of strand dissociation. This sort of quantitative experimental insights paralleled by statistical simulations impressively shade light on the rationale for strand dissociations of this novel DNA interaction process, that is an important nanomechanistic key and novel approach for the development of new chemotherapeutic agents.

Thermoresponsive Microgel-Based Free-Standing Membranes: Influence of Different Microgel Cross-Linkers on Membrane Function.

In this study we show a possibility to produce thermoresponsive, free-standing microgel membranes based on N-isopropylacrylamide (NIPAM) and the UV-sensitive comonomer 2-hydroxy-4-(methacryloyloxy)benzophenone (HMABP). To influence the final network structure and functionality of the membranes, we use different cross-linkers in the microgel syntheses and characterize the resulting structural microgel properties and the swelling behavior by means of AFM, FTIR, and PCS measurements. Varying the cross-linker results in significant changes in the structure and swelling behavior of the individual microgels and has an influence on the incorporation of the comonomer, which is essential for subsequent photochemical membrane formation. We investigate the ion transport through the different membranes by temperature-dependent resistance measurements revealing a sharp increase in resistance when the copolymer microgels reach their collapsed state. The resistance of the membranes can be adjusted by different cross-linkers and the associated incorporation of the comonomer. Furthermore, we show that transferring a reversible cross-linker from a cross-linked state to an un-cross-linked state strongly influences the membrane properties and even reverses the switching behavior, while the mechanical stability of the membrane is maintained.

Tuning Xanthan Viscosity by Directed Random Coil-to-Helix Transition.

Xanthan gum is a polysaccharide that is widely used as a thickening agent in numerous food, cosmetic, and technical applications. Therefore, the knowledge of the molecular interplay that builds up and stabilizes water-binding networks is crucial for the optimization of xanthan thickening performance. Using atomic force microscopy, rheometry, and inductively coupled plasma optical emission spectroscopy, we show a clear correlation between xanthan thickening properties and the ability to form characteristic secondary structures as well as the valence and amount of cations coordinated at the polysaccharide side chain. Based on these findings and the Debye-Hückel theory, we derive an ion-interaction model in which divalent cations mediate bridging of adjacent single polymer strands due to chelate-like coordination building stable secondary structures. We furthermore demonstrate in a cation exchange assay that xanthan secondary structures can be modified in a directed and reversible manner, which, in turn, alters its thickening properties.

Smart membranes by electron beam cross-linking of copolymer microgels.

Poly(N-isopropylacrylamide) (pNIPAM) based copolymer microgels were used to create free-standing, transferable, thermoresponsive membranes. The microgels were synthesized by copolymerization of NIPAM with N-benzylhydrylacrylamide (NBHAM). Monolayers of these colloidal gels were subsequently cross-linked using an electron gun leading to the formation of a connected monolayer. Furthermore, the cross-linked microgel layer is detached from the supporting material by dissolving the substrate. These unique systems can be used as transferable, thermoresponsive coatings and as thermoresponsive membranes. As a proof of principle for the use of such membranes we studied the ion transport through them at different temperatures revealing drastic changes when the lower critical solution temperature of the copolymer microgels is reached.

Adhesion of freshwater sponge cells mediated by carbohydrate-carbohydrate interactions requires low environmental calcium.

Marine ancestors of freshwater sponges had to undergo a series of physiological adaptations to colonize harsh and heterogeneous limnic environments. Besides reduced salinity, river-lake systems also have calcium concentrations far lower than seawater. Cell adhesion in sponges is mediated by calcium-dependent multivalent self-interactions of sulfated polysaccharide components of membrane-bound proteoglycans named aggregation factors. Cells of marine sponges require seawater average calcium concentration (10 mM) to sustain adhesion promoted by aggregation factors. We demonstrate here that the freshwater sponge Spongilla alba can thrive in a calcium-poor aquatic environment and that their cells are able to aggregate and form primmorphs with calcium concentrations 40-fold lower than that required by marine sponges cells. We also find that their gemmules need calcium and other micronutrients to hatch and generate new sponges. The sulfated polysaccharide purified from S. alba has sulfate content and molecular size notably lower than those from marine sponges. Nuclear magnetic resonance analyses indicated that it is composed of a central backbone of non- and 2-sulfated α- and ß-glucose units decorated with branches of α-glucose. Assessments with atomic force microscopy/single-molecule force spectroscopy show that S. alba glucan requires 10-fold less calcium than sulfated polysaccharides from marine sponges to self-interact efficiently. Such an ability to retain multicellular morphology with low environmental calcium must have been a crucial evolutionary step for freshwater sponges to successfully colonize inland waters.

In vitro analysis of arrhythmogenic cardiomyopathy associated desmoglein-2 (DSG2) mutations reveals diverse glycosylation patterns.

Arrhythmogenic right ventricular cardiomyopathy is a heritable cardiac disease causing severe ventricular arrhythmias, heart failure and sudden cardiac death. It is mainly caused by mutations in genes encoding several structural proteins of the cardiac desmosomes including the DSG2 gene encoding the desmosomal cadherin desmoglein-2. Although the molecular structure of the extracellular domain of desmoglein-2 is known, it remains an open question, how mutations in DSG2 contribute to the pathogenesis of arrhythmogenic right ventricular cardiomyopathy. In the present study, we analyzed the impact of different DSG2 mutations on the glycosylation pattern using de-glycosylation assays, lectin blot analysis and genetic inhibition studies. Remarkably, wildtype and mutant desmoglein-2 displayed different glycosylation patterns, although the investigated DSG2 mutations do not directly affect the consensus sequences of the N-glycosylation sites. Our study reveals complex molecular interactions between DSG2 mutations and N-glycosylations of desmoglein-2, which may contribute to the molecular understanding of the patho-mechanisms associated with arrhythmogenic right ventricular cardiomyopathy.

Biphasic Formation of 2D Nanomembranes by Photopolymerization of Diacetylene Lipids as Revealed by Infrared Difference Spectroscopy.

Two-dimensional nanomembranes are promising materials for filtration or separation by providing the basis for controlled and rapid transport between two compartments. The polymerization by UV light of diacetylene-containing lipids at an interface produces free-standing 2D nanomembranes. Here, we analyzed in situ the nanomembrane formation of 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine (DiynePC) and 1-palmitoyl-2-(10,12-tricosadiynoyl)-sn-glycero-3-phosphoethanolamine (PTPE) on germanium using light-induced infrared difference spectroscopy with attenuated total reflection to obtain insights into the kinetics and mechanism of the polymerization process. Our interpretation is supported by atomic force microscopy and density functional theory. Formation of the polymer network is evidenced by changes in the frequency of C═O stretches acting as infrared probes. However, spectral and kinetic analysis revealed a biphasic process in the monolayer. In both phases, losses in signal of CH2 stretches are observed which are not in agreement with the accepted mechanism of chain propagation for diacetylene polymerization. These signals are dominant in the second phase and are assigned to termination reactions with some contributions from intramolecular consecutive reactions. This finding now provides a spectroscopic measure for the identity and integrity of the nanomembrane complementary to microscopic analysis. We deduce that limited 2D mobility on the solid support promotes intramolecular termination, leading to smaller domains.

Correction to: Binding mechanism of anti-cancer chemotherapeutic drug mitoxantrone to DNA characterized by magnetic tweezers.

Following publication of this article [1] we found a typographical error in the results reported in the abstract. The corrected sentences should read as below.

rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations.

Recombinant adeno-associated viruses (rAAV) provide outstanding options for customization and superior capabilities for gene therapy. To access their full potential, facile genetic manipulation is pivotal, including capsid loop modifications. Therefore, we assessed capsid tolerance to modifications of the structural VP proteins in terms of stability and plasticity. Flexible glycine-serine linkers of increasing sizes were, at the genetic level, introduced into the 587 loop region of the VP proteins of serotype 2, the best studied AAV representative. Analyses of biological function and thermal stability with respect to genome release of viral particles revealed structural plasticity. In addition, insertion of the 29 kDa enzyme ß-lactamase into the loop region was tested with a complete or a mosaic modification setting. For the mosaic approach, investigation of VP2 trans expression revealed that a Kozak sequence was required to prevent leaky scanning. Surprisingly, even the full capsid modification with ß-lactamase allowed for the assembly of capsids with a concomitant increase in size. Enzyme activity assays revealed lactamase functionality for both rAAV variants, which demonstrates the structural robustness of this platform technology.

Characterization of Robust and Free-Standing 2D-Nanomembranes of UV-Polymerized Diacetylene Lipids.

Free-standing lipid membranes are promising as artificial functional membrane systems for application in separation, filtration, and nanopore sensing. To improve the mechanical properties of lipid membranes, UV-polymerized lipids have been introduced. We investigated free-standing as well as substrate-supported monolayers of 1-palmitoyl-2-(10,12-tricosadiynoyl)- sn-glycero-3-phosphoethanolamine (PTPE) and 1,2-bis(10,12-tricosadiynoyl)- sn-glycero-3-phosphocholine (DiynePC) and characterized them with respect to their structure, morphology, and stability. Using helium ion microscopy (HIM), we were able to visualize the integrity of the lipid 2D-nanomembranes spanning micrometer-sized voids under high-vacuum conditions. Atomic force microscopy (AFM) investigations under ambient conditions revealed formation of intact and robust pore-spanning 2D-nanomembranes up to 8 × 2 µm2 in size. Analysis by attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) verified a distinct reduction of signal at 2143 cm-1 from diacetylene groups in the 2D-nanomembranes after UV-polymerization. Further high-resolution AFM investigations of unpolymerized lipid monolayers revealed a well-ordered two-dimensional network, when deposited on highly oriented pyrolytic graphite (HOPG). These structures were inhibited for polymerized adlayers. Structural models for the molecular arrangement of the adlayers are proposed and discussed.

Binding mechanism of anti-cancer chemotherapeutic drug mitoxantrone to DNA characterized by magnetic tweezers.

BACKGROUND: Chemotherapeutic agents (anti-cancer drugs) are small cytostatic or cytotoxic molecules that often bind to double-stranded DNA (dsDNA) resulting in modifications of their structural and nanomechanical properties and thus interfering with the cell proliferation process. METHODS: We investigated the anthraquinone compound mitoxantrone that is used for treating certain cancer types like leukemia and lymphoma with magnetic tweezers as a single molecule nanosensor. In order to study the association of mitoxantrone with dsDNA, we conducted force-extension and mechanical overwinding experiments with a sensitivity of 10-14 N. RESULTS: Using this method, we were able to estimate an equilibrium constant of association Ka ≈ 1 × 105 M-1 as well as a binding site size of n ≈ 2.5 base pairs for mitoxantrone. An unwinding angle of mitoxantrone-intercalation of ϑ ≈ 16° was determined. CONCLUSION: Moreover, we observed a complex concentration-dependent bimodal binding behavior, where mitoxantrone associates to dsDNA as an intercalator and groove binder simultaneously at low concentrations and as a mere intercalator at high concentrations.

The novel αB-crystallin (CRYAB) mutation p.D109G causes restrictive cardiomyopathy.

Restrictive cardiomyopathy (RCM) is a rare heart disease characterized by diastolic dysfunction and atrial enlargement. The genetic etiology of RCM is not completely known. We identified by a next-generation sequencing panel the novel CRYAB missense mutation c.326A>G, p.D109G in a small family with RCM in combination with skeletal myopathy with an early onset of the disease. CRYAB encodes αB-crystallin, a member of the small heat shock protein family, which is highly expressed in cardiac and skeletal muscle. In addition to in silico prediction analysis, our structural analysis of explanted myocardial tissue of a mutation carrier as well as in vitro cell transfection experiments revealed abnormal protein aggregation of mutant αB-crystallin and desmin, supporting the deleterious effect of this novel mutation. In conclusion, CRYAB appears to be a novel RCM gene, which might have relevance for the molecular diagnosis and the genetic counseling of further affected families in the future.

Carbohydrate-Carbohydrate Interactions Mediated by Sulfate Esters and Calcium Provide the Cell Adhesion Required for the Emergence of Early Metazoans.

Early metazoans had to evolve the first cell adhesion mechanism addressed to maintain a distinctive multicellular morphology. As the oldest extant animals, sponges are good candidates for possessing remnants of the molecules responsible for this crucial evolutionary innovation. Cell adhesion in sponges is mediated by the calcium-dependent multivalent self-interactions of sulfated polysaccharides components of extracellular membrane-bound proteoglycans, namely aggregation factors. Here, we used atomic force microscopy to demonstrate that the aggregation factor of the sponge Desmapsamma anchorata has a circular supramolecular structure and that it thus belongs to the spongican family. Its sulfated polysaccharide units, which were characterized via nuclear magnetic resonance analysis, consist preponderantly of a central backbone composed of 3-α-Glc1 units partially sulfated at 2- and 4-positions and branches of Pyr(4,6)α-Gal1→3-α-Fuc2(SO3)1→3-α-Glc4(SO3)1→3-α-Glc→4-linked to the central α-Glc units. Single-molecule force measurements of self-binding forces of this sulfated polysaccharide and their chemically desulfated and carboxyl-reduced derivatives revealed that the sulfate epitopes and extracellular calcium are essential for providing the strength and stability necessary to sustain cell adhesion in sponges. We further discuss these findings within the framework of the role of molecular structures in the early evolution of metazoans.

Core-Shell Microgel-Based Surface Coatings with Linear Thermoresponse.

We study the swelling and shrinking behavior of core-shell microgels adsorbed on silicon wafers. In these systems, the core is made of cross-linked poly(N-isopropylmethacrylamide) and the shell consists of cross-linked poly(N-n-propylacrylamide). In suspension, these particles exhibit an extended linear swelling behavior in the temperature interval between the lower critical solution temperatures of the two polymers. Using ellipsometry and atomic force microscopy, we show that this linear response is also observed in the adsorbed state.

Biophysical characterization of the association of histones with single-stranded DNA.

BACKGROUND: Despite the profound current knowledge of the architecture and dynamics of nucleosomes, little is known about the structures generated by the interaction of histones with single-stranded DNA (ssDNA), which is widely present during replication and transcription. METHODS: Non-denaturing gel electrophoresis, transmission electron microscopy, atomic force microscopy, magnetic tweezers. RESULTS: Histones have a high affinity for ssDNA in 0.15M NaCl ionic strength, with an apparent binding constant similar to that calculated for their association with double-stranded DNA (dsDNA). The length of DNA (number of nucleotides in ssDNA or base pairs in dsDNA) associated with a fixed core histone mass is the same for both ssDNA and dsDNA. Although histone-ssDNA complexes show a high tendency to aggregate, nucleosome-like structures are formed at physiological salt concentrations. Core histones are able to protect ssDNA from digestion by micrococcal nuclease, and a shortening of ssDNA occurs upon its interaction with histones. The purified (+) strand of a cloned DNA fragment of nucleosomal origin has a higher affinity for histones than the purified complementary (-) strand. CONCLUSIONS: At physiological ionic strength histones have high affinity for ssDNA, possibly associating with it into nucleosome-like structures. GENERAL SIGNIFICANCE: In the cell nucleus histones may spontaneously interact with ssDNA to facilitate their participation in the replication and transcription of chromatin.

Binding mechanism of PicoGreen to DNA characterized by magnetic tweezers and fluorescence spectroscopy.

Fluorescent dyes are broadly used in many biotechnological applications to detect and visualize DNA molecules. However, their binding to DNA alters the structural and nanomechanical properties of DNA and, thus, interferes with associated biological processes. In this work we employed magnetic tweezers and fluorescence spectroscopy to investigate the binding of PicoGreen to DNA at room temperature in a concentration-dependent manner. PicoGreen is an ultrasensitive quinolinium nucleic acid stain exhibiting hardly any background signal from unbound dye molecules. By means of stretching and overwinding single, torsionally constrained, nick-free double-stranded DNA molecules, we acquired force-extension and supercoiling curves which allow quantifying DNA contour length, persistence length and other thermodynamical binding parameters, respectively. The results of our magnetic tweezers single-molecule binding study were well supported through analyzing the fluorescent spectra of stained DNA. On the basis of our work, we could identify a concentration-dependent bimodal binding behavior, where, apparently, PicoGreen associates to DNA as an intercalator and minor-groove binder simultaneously.

Nanomechanics of Fluorescent DNA Dyes on DNA Investigated by Magnetic Tweezers.

Fluorescent DNA dyes are broadly used in many biotechnological applications for detecting and imaging DNA in cells and gels. Their binding alters the structural and nanomechanical properties of DNA and affects the biological processes that are associated with it. Although interaction modes like intercalation and minor groove binding already have been identified, associated mechanic effects like local elongation, unwinding, and softening of the DNA often remain in question. We used magnetic tweezers to quantitatively investigate the impact of three DNA-binding dyes (YOYO-1, DAPI, and DRAQ5) in a concentration-dependent manner. By extending and overwinding individual, torsionally constrained, nick-free dsDNA molecules, we measured the contour lengths and molecular forces that allow estimation of thermodynamic and nanomechanical binding parameters. Whereas for YOYO-1 and DAPI the binding mechanisms could be assigned to bis-intercalation and minor groove binding, respectively, DRAQ5 exhibited both binding modes in a concentration-dependent manner.

Functional characterization of the novel DES mutation p.L136P associated with dilated cardiomyopathy reveals a dominant filament assembly defect.

BACKGROUND: Dilated cardiomyopathy (DCM) could be caused by mutations in more than 40 different genes. However, the pathogenic impact of specific mutations is in most cases unknown complicating the genetic counseling of affected families. Therefore, functional studies could contribute to distinguish pathogenic mutations and benign variants. Here, we present a novel heterozygous DES missense variant (c.407C>T; p.L136P) identified by next generation sequencing in a DCM patient. DES encodes the cardiac intermediate filament protein desmin, which has important functions in mechanical stabilization and linkage of the cell structures in cardiomyocytes. METHODS AND RESULTS: Cell transfection experiments and assembly assays of recombinant desmin in combination with atomic force microscopy were used to investigate the impact of this novel DES variant on filament formation. Desmin-p.L136P forms cytoplasmic aggregates indicating a severe intrinsic filament assembly defect of this mutant. Co-transfection experiments of wild-type and mutant desmin conjugated to different fluorescence proteins revealed a dominant affect of this mutant on filament assembly. These experiments were complemented by apertureless scanning near-field optical microscopy. CONCLUSION: In vitro analysis demonstrated that desmin-p.L136P is unable to form regular filaments and accumulate instead within the cytoplasm. Therefore, we classified DES-p.L136P as a likely pathogenic mutation. In conclusion, the functional characterization of DES-p.L136P might have relevance for the genetic counseling of affected families with similar DES mutations and could contribute to distinguish pathogenic mutations from benign rare variants.