G-quadruplexes and their ligands: Biophysical methods to unravel g-quadruplex/ligand interactions

Funding Information: (PD/00065/2013). This work was supported by PESSOA program ref. 5079 and project “Projeto de Investigação Exploratória” ref. IF/00959/2015 entitled “NCL targeting by G-quadruplex aptamers for cervical cancer therapy” financed by Fundo Social Europeu e Programa Operacional Potencial Humano. Thanks are due to FCT/MCT for the financial support of the CICS-UBI UIDB/00709/2020 research unit and to the Portuguese NMR Network (ROTEIRO/0031/2013-PINFRA/22161/2016), through national funds and, where applicable, supported by European Investment Funds FEDER through COMPETE 2020, POCI, PORL and PIDDAC.Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural-and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.publishersversionpublishe

ANÁLISE DE SIMULADORES E TECNOLOGIAS ASSISTIVAS QUE APOIAM O DESIGNER A VER COMO DALTÔNICOS

Several kinds of colorblindness limit color perception and affect how people interact with the world, especially when colors have meanings. Even with empathy, non colorblind designers have difficulties to conceive accessible interfaces for colorblind users, because they perceive colors in a different way from users. This work analyses how colorblind simulators and assistive technology can support user interface design. We conduct a search for free software on Google, on Android app store and on Chrome extension store. We identified 4 types of colorblindness simulators (filters of image, screen, sites and mobile device camera) and 3 types of assistive technologies (web sites, mobile app and CSS editor). Secrecy, internet access, time of use and other factors were considered to analyze the use of these simulators and assistive technologies as support for user interface static and dynamic analysis, during formative and summative evaluations.Os vários tipos de daltonismo limitam a percepção de cores e afetam como as pessoas interagem com o mundo, em particular quando as cores têm significados associados. Mesmo com empatia, designers não daltônicos enfrentam dificuldades para conceber interfaces acessíveis para usuários daltônicos, porque percebem as cores de uma forma distinta deles. Este trabalho analisa como simuladores e ferramentas assistivas para daltonismo podem apoiar o design de interfaces. Realizamos uma pesquisa por softwares gratuitos no Google, na loja de aplicativos do Android e na loja de extensões do navegador Chrome. Identificamos 4 tipos de simuladores de daltonismo (filtros de imagem, de tela, de sites e de câmera de dispositivo móvel) e 3 tipos de tecnologias assistivas (sites web, aplicativo móvel e editor de CSS). Sigilo, acesso à internet, tempo de uso e outros fatores foram considerados para analisar o emprego destes simuladores e tecnologias assistivas como suporte à análise estática e dinâmica de interfaces, durante avaliações formativas ou somativas

Search for alkaloids on callus culture of Passiflora alata

Preliminary work on Passiflora alata leaves failed to detect harmane alkaloids using LC. The aim of this work was to investigate the production of harmane alkaloids through the cell culture of P. alata, inducing its precursor (L-tryptophan). The leaf explants presented satisfactory results after disinfection, and the callus formation was initiated in MS media with adequate quantities of phytohormones. Sixty days after inoculation, calli were inoculated in the optimized semi-solid MS media, with and without the addition of L-tryptophan (50, 100, 200 mg/L) and kept in standard conditions for 90 days. Calli were collected on days 6, 16, 26, 36, and 90, followed by acid-base extraction, and analysed by LC. The results showed an absence of harmane, harmin, harmol, harmalol, and harmaline. With L-tryptophan feeding, two peaks were detected, collected and analysed through positive mode electrospray [ESI(+)-MS] and sequential analysis in tandem ESI(+)-MS/MS. The spectra obtained were very similar, with a repetition of the more intense ions, and consecutive loss of 68 Da units, attributed to the heterocycle pyrazole. It appeared that this transformation was not related to any enzymatic pathway previously described for the plant from L-tryptophan, and the biosynthesis of β-carboline alkaloids in callus culture of P. alata were not observed in this work.As folhas de varias espécies de Passiflora são utilizadas como ansioliticas e sedativas. Passiflora alata Curtis, Passifloraceae consta em três edições da farmacopéia brasileira, porem não há muitos estudos sobre sua composição química. No passado, enfatizava-se a ação conjunta de alcalóides e flavonóides. Em trabalho anterior, não foi detectada a presença de alcalóides harmanicos através de CLAE. Assim, decidiu-se investigar a produção dos mesmos através de cultivo celular, introduzindo seu precursor metabólico L-triptofano. Os explantes foliares apresentaram resultados satisfatorios para germinação apos assepsia, e a formação de calo foi iniciada em meio MS com quantidades adequadas de fitohormonios, previamente determinadas. Sessenta dias após a inoculação os calos foram repicados para meio semi-solido com e sem L-triptofano (50, 100, 200 mg/L), mantidos por 90 dias em condições padrão. Amostras foram coletadas com 6, 16, 26, 36, e 90 dias, realizada extração acido-base e o extrato analisado por CLAE. Os resultados mostraram a ausência de harmana, harmina, harmol, harmalol e harmalina. Dois picos presentes nas amostras com L-triptofano foram coletados e analisados através de espectrometria de massas, electrospray modo positiva [ESI(+)-MS] e analise em tandem ESI(+)-MS/MS. Os espectros correspondentes foram similares, mostrando a perda consecutiva de 68 Da, atribuídos ao pirazol. Este fato aponta para uma transformação não enzimática, não relacionada a uma biossintese previamente descrita para alcalóides β-carbolínicos.90191

Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin

PD/BD/142851/2018 PD/00065/2013 MIT-EXPL/BIO/0008/2017 IF/00959/2015One of the most significant challenges in capturing and detecting biomarkers is the choice of an appropriate biomolecular receptor. Recently, RNA G-quadruplexes emerged as plausible receptors due to their ability to recognize with high-affinity proteins. Herein, we have unveiled and characterized the capability of the precursor microRNA 149 to form a G-quadruplex structure and determined the role that some ligands may have in its folding and binding capacity to nucleolin. The G-quadruplex formation was induced by K+ ions and stabilized by ligands, as demonstrated by nuclear magnetic resonance and circular dichroism experiments. Surface plasmon resonance measurements showed a binding affinity of precursor microRNA 149 towards ligands in the micromolar range (10−5–10−6 M) and a strong binding affinity to nucleolin RNA-binding domains 1 and 2 (8.38 × 10−10 M). Even in the presence of the ligand PhenDC3, the binding remains almost identical and in the same order of magnitude (4.46 × 10−10 M). The molecular interactions of the RNA G-quadruplex motif found in precursor miRNA 149 (5′-GGGAGGGAGGGACGGG- 3′) and nucleolin RNA-binding domains 1 and 2 were explored by means of molecular docking and molecular dynamics studies. The results showed that RNA G-quadruplex binds to a cavity between domains 1 and 2 of the protein. Then, complex formation was also evaluated through polyacrylamide gel electrophoresis. The results suggest that precursor microRNA 149/ligands and precursor microRNA 149/nucleolin RNA-binding domains 1 and 2 form stable molecular complexes. The in vitro co-localization of precursor microRNA 149 and nucleolin in PC3 cells was demonstrated using confocal microscopy. Finally, a rapid and straightforward microfluidic strategy was employed to check the ability of precursor microRNA 149 to capture nucleolin RNA-binding domains 1 and 2. The results revealed that precursor microRNA 149 can capture nucleolin RNA-binding domains 1 and 2 labeled with Fluorescein 5-isothiocyanate in a concentration-dependent manner, but PhenDC3 complexation seems to decrease the ability of precursor microRNA 149 to capture the protein. Overall, our results proved the formation of the G-quadruplex structure in the precursor microRNA 149 and the ability to recognize and detect nucleolin. This proof-of-concept study could open up a new framework for developing new strategies to design improved molecular receptors for capture and detection of nucleolin in complex biological samples.publishersversionpublishe

Gestión del conocimiento. Perspectiva multidisciplinaria. Volumen 6

El libro “Gestión del Conocimiento. Perspectiva Multidisciplinaria”, Volumen 6, de la Colección Unión Global, es resultado de investigaciones. Los capítulos del libro, son resultados de investigaciones desarrolladas por sus autores. El libro es una publicación internacional, seriada, continua, arbitrada de acceso abierto a todas las áreas del conocimiento, que cuenta con el esfuerzo de investigadores de varios países del mundo, orientada a contribuir con procesos de gestión del conocimiento científico, tecnológico y humanístico que consoliden la transformación del conocimiento en diferentes escenarios, tanto organizacionales como universitarios, para el desarrollo de habilidades cognitivas del quehacer diario. La gestión del conocimiento es un camino para consolidar una plataforma en las empresas públicas o privadas, entidades educativas, organizaciones no gubernamentales, ya sea generando políticas para todas las jerarquías o un modelo de gestión para la administración, donde es fundamental articular el conocimiento, los trabajadores, directivos, el espacio de trabajo, hacia la creación de ambientes propicios para el desarrollo integral de las instituciones