Weak-cooperative binding of a long single-stranded DNA chain on a surface.

Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.

Explosive electrostatic instability of ferroelectric liquid droplets on ferroelectric solid surfaces.

We investigated the electrostatic behavior of ferroelectric liquid droplets exposed to the pyroelectric field of a lithium niobate ferroelectric crystal substrate. The ferroelectric liquid is a nematic liquid crystal, in which almost complete polar ordering of the molecular dipoles generates an internal macroscopic polarization locally collinear to the mean molecular long axis. Upon entering the ferroelectric phase by reducing the temperature from the nematic phase, the liquid crystal droplets become electromechanically unstable and disintegrate by the explosive emission of fluid jets. These jets are mostly interfacial, spreading out on the substrate surface, and exhibit fractal branching out into smaller streams to eventually disrupt, forming secondary droplets. We understand this behavior as a manifestation of the Rayleigh instability of electrically charged fluid droplets, expected when the electrostatic repulsion exceeds the surface tension of the fluid. In this case, the charges are due to the bulk polarization of the ferroelectric fluid, which couples to the pyroelectric polarization of the underlying lithium niobate substrate through its fringing field and solid-fluid interface coupling. Since the ejection of fluid does not neutralize the droplet surfaces, they can undergo multiple explosive events as the temperature decreases.

Digital Detection of Single Virus Particles by Multi-Spot, Label-Free Imaging Biosensor on Anti-Reflective Glass.

Rapid detection of whole virus particles in biological or environmental samples represents an unmet need for the containment of infectious diseases. Here, an optical device enabling the enumeration of single virion particles binding on antibody or aptamers immobilized on a surface with anti-reflective coating is described. In this regime, nanoparticles adhering to the sensor surface provide localized contributions to the reflected field that become detectable because of their mixing with the interfering waves in the reflection direction. Thus, these settings are exploited to realize a scan-free, label-free, micro-array-type digital assay on a disposable cartridge, in which the virion counting takes place in wide field-of-view imaging. With this approach we could quantify, by enumeration, different variants of SARS-CoV-2 virions interacting with antibodies and aptamers immobilized on different spots. For all tested variants, the aptamers showed larger affinity but lower specificity relative to the antibodies. It is found that the combination of different probes on the same surface enables increasing specificity of detection and dynamic range.

Correction: Surface alignment of ferroelectric nematic liquid crystals.

Correction for 'Surface alignment of ferroelectric nematic liquid crystals' by Federico Caimi et al., Soft Matter, 2021, 17, 8130-8139, https://doi.org/10.1039/D1SM00734C.

Poor concordance between definitions of type III arch and implications for risk prediction and assessment for carotid artery stenting.

OBJECTIVE: The type III arch configuration has been inconsistently reported as a stroke risk factor during carotid artery stenting. However, at least three different methods for the definition of type III arch can be identified in the literature, related to the level of the origin of the innominate artery (IA). According to Casserly's definition, a type III arch presents with an origin of the IA below the horizontal plane of the inner curvature. According to Madhwal's definition, a type III arch has a distance greater than twice the diameter of the left common carotid artery between the highest point of the arch and the origin of the IA. According to MacDonald's definition, a type III arch presents with a distance of ≥2 cm between the highest point of the arch and the origin of the IA. Our aim was to assess the level of concordance between these different methods. METHODS: Anonymized thoracic computed tomography scans of 100 healthy patients were reviewed. Two of us independently stratified the selected cases as a type I to III arch, according to the three considered definitions. The interobserver level of concordance for each type III arch classification and level of concordance among the three definitions were assessed. RESULTS: The 100 selected patients (64% male) were 76 ± 7 years old. For each definition, the interobserver repeatability was almost perfect for all three (Madhwal, κ = 0.81; 95% confidence interval [CI], 0.71-0.99; MacDonald, κ = 0.82; 95% CI, 0.72-0.92; Casserly, κ = 0.84; 95% CI, 0.74-0.93). The level of concordance among the different definitions was very low (Madhwal vs MacDonald, 85% [P = .002]; 33% for type III arch; Madhwal vs Casserly, 60% [P < .0001]; 12% for type III arch; MacDonald vs Casserly, 75% [P < .0001]; 12% for type III arch). CONCLUSIONS: The three definitions of the type III arch have a very low level of concordance, which might account for the varying clinical relevance of this configuration. Our findings have relevant implications for risk prediction for carotid artery stenting based on the presence of a type III arch, for comparisons of the results from different studies, and for comparisons of different datasets from multicenter trials.

Surface alignment of ferroelectric nematic liquid crystals.

The success of nematic liquid crystals in displays and optical applications is due to the combination of their optical uniaxiality, fluidity, elasticity, responsiveness to electric fields and controllable coupling of the molecular orientation at the interface with solid surfaces. The discovery of a polar nematic phase opens new possibilities for liquid crystal-based applications, but also requires a new study of how this phase couples with surfaces. Here we explore the surface alignment of the ferroelectric nematic phase by testing different rubbed and unrubbed substrates that differ in coupling strength and anchoring orientation and find a variety of behaviors - in terms of nematic orientation, topological defects and electric field response - that are specific to the ferroelectric nematic phase and can be understood as a consequence of the polar symmetry breaking. In particular, we show that by using rubbed polymer surfaces it is easy to produce cells with a planar polar preferential alignment and that cell electrostatics (e.g. grounding the electrodes) has a remarkable effect on the overall homogeneity of the ferroelectric ordering.

Yield stress "in a flash": investigation of nonlinearity and yielding in soft materials with an optofluidic microrheometer.

Yield stress materials deform as elastic solids or flow as viscous liquids, depending on the applied stress, which also allows them to trap particles below a certain size or density threshold. To investigate the conditions for such a transition at the microscale, we use an optofluidic microrheometer, based on the scattering of an infrared beam onto a microbead, which reaches forces in the nN scale. We perform creep experiments on a model soft material composed of swollen microgels, determining the limits of linear response and yield stress values, and observe quantitative agreement with bulk measurements. However, the motion of the microbead, both below and above yielding, reflects distinctive microscale features of the surrounding material, whose plastic rearrangements were investigated by us using small, passive tracers.

A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA.

Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding-equilibrium and kinetics-by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4-DNA interactions. We found a strong enthalpy-entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4.

Gelling without Structuring: A SAXS Study of the Interactions among DNA Nanostars.

We evaluate, by means of synchrotron small-angle X-ray scattering, the shape and mutual interactions of DNA tetravalent nanostars as a function of temperature in both the gas-like state and across the gel transition. To this end, we calculate the form factor from coarse-grained molecular dynamics simulations with a novel method that includes hydration effects; we approximate the radial interaction of DNA nanostars as a hard-sphere potential complemented by a repulsive and an attractive Yukawa term; and we predict the structure factors by exploiting the perturbative random phase approximation of the Percus-Yevick equation. Our approach enables us to fit all the data by selecting the particle radius and the width and amplitude of the attractive potential as free parameters. We determine the evolution of the structure factor across gelation and detect subtle changes of the effective interparticle interactions, that we associate to the temperature and concentration dependence of the particle size. Despite the approximations, the approach here adopted offers new detailed insights into the structure and interparticle interactions of this fascinating system.

Type III Arch Configuration as a Risk Factor for Carotid Artery Stenting: A Systematic Review of Contemporary Guidelines on Management of Carotid Artery Stenosis.

BACKGROUND: Type III arch configuration is frequently reported as a stroke risk factor for carotid angioplasty and stenting (CAS). We reviewed contemporary guidelines on management of carotid artery stenosis to assess the clinical relevance attributed to this anatomic feature in current clinical practice. METHODS: The study was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. The PubMed, EMBASE, and Web of Science databases were searched to identify all guidelines on extracranial carotid disease published between January 2008 and March 2020. A total of 435 articles were screened. For multiple guidelines from the same writing group, only the most recent updated version was considered. Eighteen documents were identified for qualitative analysis. RESULTS: Four guidelines specifically reported type III arch as a predictive factor of periprocedural complications after CAS. Two of them also provided a low level of evidence of their recommendation. None of the documents indicated the exact criteria for aortic arch classification. Three different methods to describe type III arch configuration were identified. CONCLUSIONS: Type III arch configuration is inconsistently included among stroke risk factors for CAS in contemporary guidelines, and variably defined. Further studies on the level of concordance between the 3 existing definition criteria are warranted.

Quadruplex knots as network nodes: nano-partitioning of guanosine derivates in supramolecular hydrogels.

Aqueous solutions of guanosine-5'-monophosphates (GMP) - known to form G-quadruplexes and liquid crystal phases - can be induced to turn into high water content gels by the addition of guanosine (Gua). By a combination of Light Scattering (LS) and AFM we show that Gua/GMP hydrogels are microscopically heterogeneous, formed by Gua-rich disordered microcoils of intertwined filaments ("knots") connected by GMP-rich long linear threads. The different thermal stability of knots and threads controls the gel transition.

Newtonian to non-newtonian fluid transition of a model transient network.

The viscosity of gel-forming fluids is notoriously complex and its study can benefit from new model systems that enable a detailed control of the network features. Here we use a novel and simple microfluidic-based active microrheology approach to study the transition from Newtonian to non-Newtonian behavior in a DNA hydrogel whose structure, connectivity, density of bonds, bond energy and kinetics are strongly temperature dependent and well known. In a temperature range of 15 °C, the system reversibly and continuously transforms from a Newtonian dispersion of low-valence nanocolloids into a strongly shear-thinning fluid, passing through a set of intermediate states where it behaves as a power-law fluid. We demonstrate that the knowledge of network topology and bond free energy enables to quantitatively predict the observed behavior using established rheology models.

Fluctuating Elasticity Mode in Transient Molecular Networks.

Transient molecular networks, a class of adaptive soft materials with remarkable application potential, display complex, and intriguing dynamic behavior. By performing dynamic light scattering on a wide angular range, we study the relaxation dynamics of a reversible network formed by DNA tetravalent nanoparticles, finding a slow relaxation mode that is wave vector independent at large q and crosses over to a standard q^{-2} viscoelastic relaxation at low q. Exploiting the controlled properties of our DNA network, we attribute this mode to fluctuations in local elasticity induced by connectivity rearrangement. We propose a simple beads and springs model that captures the basic features of this q^{0} behavior.

Nonlinear diffusion model for annealed proton-exchanged waveguides in zirconium-doped lithium niobate.

Photorefractive-damage- (PRD) resistant zirconium-oxide-doped lithium niobate is investigated as a substrate for the realization of annealed proton-exchanged (APE) waveguides. Its advantages are a favorable distribution coefficient, PRD resistance comparable to magnesium-oxide-doped lithium niobate, and a proton-diffusion behavior resembling congruent lithium niobate. A 1D model for APE waveguides was developed based on a previous model for congruently melting lithium niobate. Evidence for a nonlinear index dependence on concentration was found.

Equilibrium gels of low-valence DNA nanostars: a colloidal model for strong glass formers.

Kinetic arrest in colloidal dispersions with isotropic attractive interactions usually occurs through the destabilization of the homogeneous phase and the formation of a non-equilibrium network of jammed particles. Theory and simulations predict that a different route to gelation should become available when the valence of each colloidal particle is suitably reduced. Under these conditions, gelation should be achievable through a reversible sequence of equilibrium states. Here we report the reversible dynamic arrest of a dispersion of DNA-based nanoparticles with anisotropic interactions and a coordination number equal to four. As the temperature is decreased, the relaxation time for density fluctuations slows down by about five orders of magnitude, following an Arrhenius scaling in the entire experimentally accessible temperature window. The system is in thermodynamic equilibrium at all temperatures. Gelation in our system mimics the dynamic arrest of networking atomic strong glass formers such as silica, for which it could thus provide a suitable colloidal model.

Serum antibody fingerprinting of SARS-CoV-2 variants in infected and vaccinated subjects by label-free microarray biosensor.

Both viral infection and vaccination affect the antibody repertoire of a person. Here, we demonstrate that the analysis of serum antibodies generates information not only on the virus type that caused the infection but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from the plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fractions. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed a larger quantity of total Ig and a lower fraction of IgA relative to the population of convalescent unvaccinated subjects.

Walking Ferroelectric Liquid Droplets with Light.

The motion of ferroelectric liquid sessile droplets deposited on a ferroelectric lithium niobate substrate can be controlled by a light beam of moderate intensity irradiating the substrate at a distance of several droplet diameters from the droplet itself. The ferroelectric liquid is a nematic liquid crystal, in which almost complete polar ordering of the molecular dipoles generates an internal macroscopic polarization locally collinear to the mean molecular long axis. Upon entering the ferroelectric phase, droplets are either attracted toward the center of the beam or repelled, depending on the side of the lithium niobate exposed to light irradiation. Moreover, moving the beam results in walking the ferroelectric droplet over long distances on the substrate. This behavior is understood as due to the coupling between the polarization of the ferroelectric droplet and the polarization photoinduced in the irradiated region of the lithium niobate substrate. Indeed, the effect is not observed in the conventional nematic phase, suggesting the crucial role of the ferroelectric liquid crystal polarization.

Soft proton exchanged channel waveguides in congruent lithium tantalate for frequency doubling.

We report on stable optical waveguides fabricated by soft-proton exchange in periodically-poled congruent lithium tantalate in the α-phase. The channel waveguides are characterized in the telecom wavelength range in terms of both linear properties and frequency doubling. The measurements yield a nonlinear coefficient of about 9.5 pm/V, demonstrating that the nonlinear optical properties of lithium tantalate are left nearly unaltered by the process.

Elasticity and Viscosity of DNA Liquid Crystals.

Concentrated solutions of blunt-ended DNA oligomer duplexes self-assemble in living polymers and order into lyotropic nematic liquid crystal phase. Using the optical torque provided by three distinct illumination geometries, we induce independent splay, twist, and bend deformations of the DNA nematic and measure the corresponding elastic coefficients K1, K2, and K3, and viscosities ηsplay, ηtwist, and ηbend. We find the viscoelasticity of the system to be remarkably soft, as the viscoelastic coefficients are smaller than in other lyotropic liquid crystals. We find K1 > K3 > K2, in agreement with the elasticity of the nematic phase of flexible polymers, and ηbend > ηsplay > ηtwist a behavior that is nonconventional in the context of chromonic, polymeric, and thermotropic liquid crystals, indicating a possible role of the weakness and reversibility of the DNA aggregates.