RNAGCN: RNA tertiary structure assessment with a graph convolutional network

RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to predict RNA 3D structures. For these methods, designing a model or scoring function for structure quality assessment is an essential step but this step poses challenges. In this study, we designed and trained a deep learning model to tackle this problem. The model was based on a graph convolutional network (GCN) and named RNAGCN. The model provided a natural way of representing RNA structures, avoided complex algorithms to preserve atomic rotational equivalence, and was capable of extracting features automatically out of structural patterns. Testing results on two datasets convincingly demonstrated that RNAGCN performs similarly to or better than four leading scoring functions. Our approach provides an alternative way of RNA tertiary structure assessment and may facilitate RNA structure predictions. RNAGCN can be downloaded from https://gitee.com/dcw-RNAGCN/rnagcn.     

Dielectric loss and electromagnetic absorption performance study of 1T/2H-MoS2/Mo2S3 nanocomposites with different ratios

High dielectric loss materials have an important application in electromagnetic (EM) absorption fields. In this paper, the ternary nanocomposites: 1T/2H-MoS₂/Mo₂S₃ with heterogeneous interfaces are synthesized by hydrothermal method. XRD, XPS, FTIR, SEM, and TEM measurements are applied to study the structure, morphology, and composition. The frequency spectra of complex permittivity (ε_r-f) are measured in 2–18 GHz by vector network analyzer. The results show that the nanocomposites have higher dielectric loss angle tangents than the reported 2H-MoS₂ absorbers. Based on the ε_r-f spectra, the reflection loss-frequency curves ($RL-f$) are simulated at given thicknesses. An effective absorption bandwidth of 5.2 GHz (12.8–18 GHz) and a $RL$ peak of −29.49 dB are achieved in a thin thickness of 1.62 mm, which are comparable to the reported 2H-MoS₂ absorbers with complex composition, showing that the 1T/2H-MoS₂/Mo₂S₃ nanocomposites have great application potential as an EM wave absorber in the K_u band.     

Aromatic 19F–13C TROSY—[19F, 13C]-Pyrimidine Labeling for NMR Spectroscopy of RNA

We present the access to [5-¹⁹F, 5-¹³C]-uridine and -cytidine phosphoramidites for the production of site-specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5-¹⁹F, 5-¹³C]-pyrimidine labels into five RNAs—the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ϵ (hHBV ϵ) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre-microRNA (miRNA) 21 and the 59 nt full length pre-miRNA 21. The main stimulus to introduce the aromatic ¹⁹F–¹³C-spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole-dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic ¹³C–¹⁹F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5-¹⁹F, 5-¹³C]/[5-¹⁹F] pyrimidine labeling. For the 61 nt hHBV ϵ we find a beneficial ¹⁹F–¹³C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [¹⁹F, ¹³C]-labeling of the SAM VI aptamer domain and the pre-miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.     

Guanidine‐Based Polymer Brushes Grafted onto Silica Nanoparticles as Efficient Artificial Phosphodiesterases

Polymer brushes grafted to the surface of silica nanoparticles were fabricated by atom‐transfer radical polymerization (ATRP) and investigated as catalysts in the cleavage of phosphodiesters. The surfaces of silica nanoparticles were functionalized with an ATRP initiator. Surface‐initiated ATRP reactions, in varying proportions, of a methacrylate moiety functionalized with a phenylguanidine moiety and an inert hydrophilic methacrylate species afforded hybrid nanoparticles that were characterized with potentiometric titrations, thermogravimetric analysis, and SEM. The activity of the hybrid nanoparticles was tested in the transesterification of the RNA model compound 2‐hydroxypropyl para‐nitrophenylphosphate (HPNP) and diribonucleoside monophosphates. A high catalytic efficiency and a remarkable effective molarity, thus overcoming the effective molarities previously observed for comparable systems, indicate the existence of an effective cooperation of the guanidine/guanidinium units and a high level of preorganization in the nanostructure. The investigated system also exhibits a marked and unprecedented selectivity for the diribonucleoside sequence CpA. The results presented open up the way for a novel and straightforward strategy for the preparation of supramolecular catalysts.     

Human-to-metal electrostatic discharge current measurements – Notes on the ESD current waveform

The Electrostatic Discharge (ESD) phenomenon has been described through the IEC 61000-4-2. ESD current parameters' values, have been set in this Standard. The theoretical ESD current waveform defined in this standard, describing the conventional Contact discharge mode, needs to be re-evaluated on the basis of accurate experimental data. Even though the standard deals with commercial ESD generators, its goal is to simulate the natural phenomenon as good as possible. More and accurate data may contribute to the better simulation of the natural phenomenon. New values and better comprehension of the phenomenon demand new measurements based on high end measuring equipment. Such works and publications have been carried out the past years. Yet, the need to systematize and integrate this work remains. Larger and trust-worthy series of measurements need to be carried out and presented clearly.This paper deals with new ESD-current data, taken with broadband equipment. New and more detailed measurements like these, were never before taken at such a large number of individuals. The goal of this work is that the data acquired can serve as a basis for re-evaluating the conventional approach of the scientific community to the ESD event.In this paper, using a broadband measuring system, new parameters' values are measured and relations are presented, following standard statistical procedures. The results, which occur from measurements carried out on tenths of human individuals, are questioning the Standard in many points. A new way of approaching the standardization of the ESD current is proposed, as the excuse of the poor measuring equipment that sets barriers on the measuring accuracy, does not apply any more. The charging voltages of 500 V and 1000 V were also examined since such range of voltages are often met at ESD events and they are considered very harmful.     

Gapmer Antisense Oligonucleotides Containing 2′,3′-Dideoxy-2′-fluoro-3′-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing

Off-target effects remain a significant challenge in the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the years various modifications have been synthesized and incorporated into AONs, however, precise control of RNase H-induced cleavage and target sequence selectivity has yet to be realized. Herein, the synthesis of the uracil and cytosine derivatives of a novel class of 2′-deoxy-2′-fluoro-3′-C-hydroxymethyl-β-d -lyxo-configured nucleotides has been accomplished and the target molecules have been incorporated into AONs. Experiments on exonuclease degradation showed improved nucleolytic stability relative to the unmodified control. Upon the introduction of one or two of the novel 2′-fluoro-3′-C-hydroxymethyl nucleotides as modifications in the gap region of a gapmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably, a tailored single cleavage event could be engineered depending on the positioning of a single modification. The effect of single mismatched base pairs was scanned along the full gap region demonstrating that the modification enables a remarkable specificity of RNase H cleavage. A cell-based model system was used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.