Synthesis of Janus compounds for the recognition of G-U mismatched nucleobase pairs

The design and synthesis of two Janus-type heterocycles with the capacity to simultaneously recognize guanine and uracyl in G-U mismatched pairs through complementary hydrogen bond pairing is described. Both compounds were conveniently functionalized with a carboxylic function and efficiently attached to a tripeptide sequence by using solid-phase methodologies. Ligands based on the derivatization of such Janus compounds with a small aminoglycoside, neamine, and its guanidinylated analogue have been synthesized, and their interaction with Tau RNA has been investigated by using several biophysical techniques, including UV-monitored melting curves, fluorescence titration experiments, and 1H NMR. The overall results indicated that Janus-neamine/guanidinoneamine showed some preference for the +3 mutated RNA sequence associated with the development of some tauopathies, although preliminary NMR studies have not confirmed binding to G-U pairs. Moreover, a good correlation has been found between the RNA binding affinity of such Janus-containing ligands and their ability to stabilize this secondary structure upon complexation

Accurate classification of RNA structures using topological fingerprints

While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC \u3e 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint

Conjugation of a Ru(II) Arene Complex to Neomycin or to Guanidinoneomycin Leads to Compounds with Differential Cytotoxicities and Accumulation between Cancer and Normal Cells

A straightforward methodology for the synthesis of conjugates between a cytotoxic organometallic ruthenium(II) complex and amino- and guanidinoglycosides, as potential RNA-targeted anticancer compounds, is described. Under microwave irradiation, the imidazole ligand incorporated on the aminoglycoside moiety (neamine or neomycin) was found to replace one triphenylphosphine ligand from the ruthenium precursor [(η6-p-cym)RuCl(PPh3)2]+, allowing the assembly of the target conjugates. The guanidinylated analogue was easily prepared from the neomycin-ruthenium conjugate by reaction with N,N′-di-Boc-N″-triflylguanidine, a powerful guanidinylating reagent that was compatible with the integrity of the metal complex. All conjugates were purified by semipreparative high-performance liquid chromatography (HPLC) and characterized by electrospray ionization (ESI) and matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and NMR spectroscopy. The cytotoxicity of the compounds was tested in MCF-7 (breast) and DU-145 (prostate) human cancer cells, as well as in the normal HEK293 (Human Embryonic Kidney) cell line, revealing a dependence on the nature of the glycoside moiety and the type of cell (cancer or healthy). Indeed, the neomycin-ruthenium conjugate (2) displayed moderate antiproliferative activity in both cancer cell lines (IC50 ≈ 80 μM), whereas the neamine conjugate (4) was inactive (IC50 ≈ 200 μM). However, the guanidinylated analogue of the neomycin-ruthenium conjugate (3) required much lower concentrations than the parent conjugate for equal effect (IC50 = 7.17 μM in DU-145 and IC50 = 11.33 μM in MCF-7). Although the same ranking in antiproliferative activity was found in the nontumorigenic cell line (3 2 > 4), IC50 values indicate that aminoglycoside-containing conjugates are about 2-fold more cytotoxic in normal cells (e.g., IC50 = 49.4 μM for 2) than in cancer cells, whereas an opposite tendency was found with the guanidinylated conjugate, since its cytotoxicity in the normal cell line (IC50 = 12.75 μM for 3) was similar or even lower than that found in MCF-7 and DU-145 cancer cell lines, respectively. Cell uptake studies performed by ICP-MS with conjugates 2 and 3 revealed that guanidinylation of the neomycin moiety had a positive effect on accumulation (about 3-fold higher in DU-145 and 4-fold higher in HEK293), which correlates well with the higher antiproliferative activity of 3. Interestingly, despite the slightly higher accumulation in the normal cell than in the cancer cell line (about 1.4-fold), guanidinoneomycin-ruthenium conjugate (3) was more cytotoxic to cancer cells (about 1.8-fold), whereas the opposite tendency applied for neomycin-ruthenium conjugate (2). Such differences in cytotoxic activity and cellular accumulation between cancer and normal cells open the way to the creation of more selective, less toxic anticancer metallodrugs by conjugating cytotoxic metal-based complexes such as ruthenium(II) arene derivatives to guanidinoglycosides

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N [subscript G] is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε ε[subscript s] with slow internal dynamics. The cohesion strength ε[subscript s] of this freezing transition depends on N G . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N [subscript G] . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi

Analysing the Impact of Regulation on Disruptive Innovations: The Case of Wireless Technology

The paper analyses the role of regulation in the suppression of disruptive innovations and shows that this process might be explained by the dependance on the path of joint evolution of regulation and the mainstream technology. Industrial policy in highly regulated industries such as wireless telecommunications is able to support evolution of established technologies and adjust itself to sustaining innovations, while regulatory disconnection impedes disruptive technologies, and the market plays a quite secondary role in this process. We observe more innovations in those parts of telecommunications where regulator is less active, but the core, the physical layer, of the industry is changing in sustaining way of development of the technology. The paper argues that the problem of impediment to disruptive innovations could be alleviated if the crucial resources of the industry were accessible for a number of potential innovators and newcomers. The openness makes easier the appearance of disruptive technologies, and regulation must facilitate it in order to promote opportunities for creative destruction

Solution structure of the HIV-1 frameshift inducing stem-loop RNA

This paper examines the economic motivations, and the economic and biophysical effects, of the adoption of large-scale irrigation in the Spanish Mediterranean coast via a case study of the municipality of Vilassar de Mar (Barcelona) between 1850 and 1937. A balance sheet of the economic gains of the harvested biomass and associated energy usage prior to and after the introduction of irrigation during the first decades of the 20th century allows us to understand the causes and consequences surrounding the adoption of this new intensive agriculture. Based on the cultivation of new horticultural crops with a high demand on the international market, the new intensive agriculture provided peasants higher economic profits and produced a larger amount of biomass and associated energy.En este artículo se estudian los motivos económicos y efectos, tanto económicos como biofísicos, de la introducción del regadío a gran escala en la agricultura litoral mediterránea, a partir de un estudio de caso, a saber, el municipio de Vilassar de Mar (Barcelona) entre 1850 y 1937. El cálculo de los balances económicos de la agricultura, y de la biomasa cosechada y energía asociada, antes y después de la introducción del regadío en las primeras décadas del siglo XX, permite obtener un mayor conocimiento de las causas y consecuencias de la opción por esta nueva agricultura intensiva. Una agricultura intensiva, basada en la producción de cultivos hortícolas de gran demanda internacional, que proporcionaba a los agricultores mayores beneficios económicos y producía una mayor cantidad de biomasa cultivada y energía asociada

Evaluation of potential severe accidents during low power and shutdown operations at Grand Gulf, Unit 1: Summary of results. Volume 1

During 1989 the Nuclear Regulatory Commission (NRC) initiated an extensive program to examine the potential risks during low power and shutdown operations. Two plants, Surry and Grand Gulf, were selected as the plants to be studied by Brookhaven National Laboratory (Surry) and Sandia National Laboratories (Grand Gulf). This report documents the work performed during the analysis of the Grand Gulf plant. A phased approach was used for the overall study. In Phase 1, the objectives were to identify potential vulnerable plant configurations, to characterize (on a high, medium, or low basis) the potential core damage accident scenario frequencies and risks, and to provide a foundation for a detailed Phase 2 analysis. It was in Phase 1 that the concept of plant operational states (POSs) was developed to allow the analysts to better represent the plant as it transitions from power operation to nonpower operation than was possible with the traditional technical specification divisions of modes of operation. This phase consisted of a coarse screening analysis performed for all POSs, including seismic and internal fire and flood for some POSs. In Phase 2, POS 5 (approximately cold shutdown as defined by Grand Gulf Technical Specifications) during a refueling outage was selected as the plant configuration to be analyzed based on the results of the Phase 1 study. The scope of the Level 1 study includes plant damage state analysis and uncertainty analysis and is documented in a multi-volume NUREG/CR report (i.e., NUREG/CR-6143). The internal events analysis is documented in Volume 2. Internal fire and internal flood analyses are documented in Volumes 3 and 4, respectively. A separate study on seismic analysis, documented in Volume 5, was performed for the NRC by Future Resources Associates, Inc. The Level 2/3 study of the traditional internal events is documented in Volume 6, and a summary of the results for all analyses is documented in Volume 1

Atomic Energy Commission Report AECD-4212

The following report discusses a method to analyze boron in TF6, including an evaporation method for developing the boron-curcumin color and distillation of boron in TF6 samples