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To ensure specificity of small interfering RNAs (siRNAs), the antisense strand must be selected by the RNA-induced silencing complex (RISC). We have previously demonstrated that a 5'-morpholino-modified nucleotide at the 5'-end of the sense strand inhibits its interaction with RISC ensuring selection of the desired antisense strand. To improve this antagonizing binding property even further, a new set of morpholino-based analogues, Mo2 and Mo3, and a piperidine analogue, Pip, were designed based on the known structure of Argonaute2, the slicer enzyme component of RISC. Sense strands of siRNAs were modified with these new analogues, and the siRNAs were evaluated in vitro and in mice for RNAi activity. Our data demonstrated that Mo2 is the best RISC inhibitor among the modifications tested and that it effectively mitigates sense strand-based off-target activity of siRNA.

The analysis of nuclear magnetic resonance (NMR) spectra to detect peaks and characterize their parameters, often referred to as deconvolution, is a crucial step in the quantification, elucidation, and verification of the structure of molecular systems. However, deconvolution of 1D NMR spectra is a challenge for both experts and machines. We propose a robust, expert-level quality deep learning-based deconvolution algorithm for 1D experimental NMR spectra. The algorithm is based on a neural network trained on synthetic spectra. Our customized pre-processing and labeling of the synthetic spectra enable the estimation of critical peak parameters. Furthermore, the neural network model transfers well to the experimental spectra and demonstrates low fitting errors and sparse peak lists in challenging scenarios such as crowded, high dynamic range, shoulder peak regions as well as broad peaks. We demonstrate in challenging spectra that the proposed algorithm is superior to expert results., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: All authors except Jan Dirk Wegner, Roland Sigel and Helmut Grabner report financial support was provided by Innosuisse Swiss Innovation Agency. All authors from Bruker Switzerland AG report a relationship with Bruker BioSpin AG that includes: employment., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

For light propagation in a layered refractive index profile, critical conditions occur when the wave vector perpendicular to the layering becomes zero. Such conditions can occur in a total reflection geometry. Conventional transfer matrix methods become singular, and geometrical optics concepts break down at critical conditions. We introduce two new, to the best of our knowledge, basis systems using virtual linear functions that obey the Helmholtz equation and turn to linear functions required for critical conditions.

The statistical presence of kinks which form defects in semi-flexible polymer chains leads to a polydispersity in the effective persistence length. The form factor of a distorted semi-flexible polymer results as an average over this persistence polydispersity. It turns out that the scattering behavior of an ensemble of distorted semi-flexible polymer chains is quite well approximated by a form factor of an undistorted chain with a R g -equivalent persistence length. An apparent length polydispersity is observed for short distorted chains. The R g -equivalent persistence length is significantly smaller than the innate persistence length multiplied by the fraction of regular monomers. The results are compared to related work on DNA from the literature.

RNA molecules fold into complex structures that allow them to perform specific functions. To compensate the relative lack of diversity of functional groups within nucleotides, metal ions work as crucial co-factors. In addition, shifted pK a s are observed in RNA, enabling acid-base reactions at ambient pH. The central catalytic domain 5 (D5) hairpin of the Azotobacter vinelandii group II intron undergoes both metal ion binding and pH dependence, presumably playing an important functional role in the ribozyme's reaction. By NMR spectroscopy we have here characterized the metal ion binding sites and affinities for the hairpin's internal G-A mismatch, bulge, and pentaloop. The influence of Mg(ii) and pH on the local conformation of the catalytically crucial region is also explored by fluorescence spectroscopy.

Concepts and opportunities of interfaces with soft properties are discussed. Such interfaces show a strong response to external fields. How can the interface tension which governs interfacial behavior become compatible with soft and fluctuating degrees of freedom at the interface?

An experimental strategy for the detection of fluctuation dynamics at interfaces based on a combination of photon correlation spectroscopy (PCS) with a nulling ellipsometry scheme is investigated theoretically. The intensity description of ellipsometry measurements is generalized to PCS time correlation functions. The nulling ellipsometry procedure is applied for every lag time t of the correlation functions, to extract the dynamics connected to the coherent signal which contains the interface dynamics. The classical ellipsometry parameters Δ and tanΨ are generalized to functions and tan [capital Psi, Greek, tilde] Q (t). A suitable Siegert relation is derived and employed to show that either field correlation functions or intensity correlation functions after baseline subtraction can be used as the starting point for the nulling ellipsometry procedure.

Riboswitches are cis-regulatory RNA elements on the mRNA level that control the expression of the downstream coding region. The interaction of the riboswitch with its specific metabolite, which is related to the function of the controlled gene, induces a structural change of the RNA architecture. Consequently, gene regulation is induced by un/masking of the ribosome binding site (RBS). In the genome of Klebsiella pneumoniae a sequence was identified by bioinformatics and proposed to be a B12 riboswitch regulated by coenzyme B12. Here we study this new coenzyme B12-dependent riboswitch system by in-line probing and ITC. The riboswitch sequence includes the whole expression platform as well as RBS. In-line probing experiments were performed to investigate the structural rearrangement of this 243-nt long RNA sequence while Isothermal Titration Calorimetry (ITC) yielded the thermodynamic parameters of the interaction between the riboswitch and its metabolite. The interaction of coenzyme B12 with the butB riboswitch of K. pneumoniae is an exothermic process with a 1:1 binding stoichiometry and binding affinities of log KA=6.73±0.02 at 15°C and log KA=6.00±0.09 at 30°C., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Dynamic light scattering (DLS) was performed on dilute suspensions of colloidal particles, where the scattering intensity was minimised by ellipsometric optics as in ellipsometric light scattering. Measurements at minimum intensity settings are dominated by the incoherent scattering properties, i.e. the deviations from the average scattering properties. The observed relaxation dynamics does not vary with the scattering angle, but depends on the wavelength λ of the employed light. Therefore, the process has a λ-dependence beyond the dependence included in the scattering vector. Such incoherent ellipsometric DLS could be applied to determine the residence time of particles in volumes with an extension comparable to λ, and to obtain detailed information on the dynamics of complex systems which is usually hidden by the dominating diffusive process.

Phosphating is a crucial process in the corrosion protection of metals. Here, activation and fluoride-assisted tricationic phosphating is investigated on aluminum-silicon (AS) coated steel surfaces. Dynamic light scattering results from the activation bath show a bimodal size distribution, with hydrodynamic radii of ~400 nm and ~10 μm. For the smaller particle fraction, static light scattering results are consistent with the interpretation of disklike particles as scattering objects. Particles of the larger fraction sediment with time. In the presence of electrolyte, the scattering intensity from the larger particle fraction increases. Coagulation with time is suggested to be related to the decrease in activity of the activation bath. Scanning Auger microscopy (SAM) shows a higher phosphorus concentration after titanium phosphate activation in the Al-rich areas compared to the Si-rich areas of the AS coatings. There is no correlation between the size of the species in the activation bath, and the size of the phosphate-containing regions on the activated surface. Phosphating was performed in the presence of hexafluorosilicic acid, H2SiF6, ammonium hydrogen difluoride, NH4HF2, and both, at an initial pH of 2.5. The absence of crystals after phosphating with H2SiF6 is an indication that SiF6(2-) is the final product of the oxide dissolution in the presence of fluoride. In the presence of NH4HF2, the Si-rich regions of the surface are phosphated before the Si-poor (Al-rich) regions. Hence, the phosphate distribution after activation and after phosphating are opposite. These results show that a high surface concentration of phosphate after activation is not sufficient for a high coverage with phosphate crystals after phosphating.

Through the use of Mie theory generalized to multiple spheres, the derivatives of the scattering matrix elements and ellipsometric scattering variables are found as a function of shell thickness and nonconcentricity for core-shell particles. In particular, for the case of a core-shell sphere system where the centers are not concentric, the derivatives are taken with respect to the line segment describing the distance between spherical centers. The derivatives of the scattering matrix elements can be used to calculate the changes in ellipsometric light scattering, allowing for sensitivity and precision in quantitative models of fluctuations in core-shell systems. Computed results giving model contrast for a variety of sizes and fluctuation modes are used to design and guide novel light-scattering experiments currently underway.

Two polyisoprene-polyethyleneoxide diblock copolymers with different block length ratios adsorbed to the water surface were investigated by multiple angle of incidence ellipsometry, evanescent wave light scattering, and surface tension experiments. In a semidilute interfacial regime, the transition from a two-dimensional to a "mushroom" regime, in which polymer chains form loops and tails in the subphase, was discussed. A diffusion mechanism parallel to the interface was probed by evanescent wave dynamic light scattering. At intermediate concentrations, the interfacial diffusion coefficient D(∥) scales with the surface concentration Γ, as D(∥) ~ Γ(0.77) in agreement with the scaling observed for polymer solutions in a semidilute regime. At relatively high concentrations a decreasing of D(∥) is discussed in terms of increasing friction due to interactions between polyisoprene chains., (Copyright © 2010 Elsevier Inc. All rights reserved.)

A light-scattering goniometer for evanescent-wave dynamic light scattering (EWDLS) measurements at a liquid-fluid interface is introduced, and used for measurements on two charge-stabilized polystyrene colloid systems adsorbed to alkane-water interfaces. The goniometer allows an independent variation of the penetration depth and the scattering vector components parallel and perpendicular to a liquid-fluid interface. The possible illumination geometries are compared. Ellipsometry at the liquid-fluid interface is implemented as a complementary tool. In EWDLS measurements, the absence of diffusive motion perpendicular to the interface is demonstrated, which confirms the adsorption of the particles. The two-step decay of the autocorrelation function is interpreted in terms of diffusion within a two-dimensional interface lattice of colloidal particles, stabilized by repulsive electrostatic interactions, and a desorption process. A significant slowing down of the in-plane diffusion of the colloids as compared to the bulk diffusion is observed.