Showing papers by "Alfredo Berzal-Herranz published in 2014"
TL;DR: The preservation of this RNA–RNA interacting network, and the maintenance of the proper balance between different contacts, may play a crucial role in the switch between different steps of the HCV cycle.
Abstract: The hepatitis C virus (HCV) RNA genome contains multiple structurally conserved domains that make long-distance RNA-RNA contacts important in the establishment of viral infection. Microarray antisense oligonucleotide assays, improved dimethyl sulfate probing methods and 2' acylation chemistry (selective 2'-hydroxyl acylation and primer extension, SHAPE) showed the folding of the genomic RNA 3' end to be regulated by the internal ribosome entry site (IRES) element via direct RNA-RNA interactions. The essential cis-acting replicating element (CRE) and the 3'X-tail region adopted different 3D conformations in the presence and absence of the genomic RNA 5' terminus. Further, the structural transition in the 3'X-tail from the replication-competent conformer (consisting of three stem-loops) to the dimerizable form (with two stem-loops), was found to depend on the presence of both the IRES and the CRE elements. Complex interplay between the IRES, the CRE and the 3'X-tail region would therefore appear to occur. The preservation of this RNA-RNA interacting network, and the maintenance of the proper balance between different contacts, may play a crucial role in the switch between different steps of the HCV cycle.
55 citations
TL;DR: Intracellular stability studies showed that the highest stabilization effects were obtained when the DNAzymes′ cores were jointly modified with 2′‐C‐methyl‐ and 2‐O‐methylnucleosides, yielding an increase by up to fivefold in the total DNAzyme accumulation within the cell milieu within 48 h of transfection.
Abstract: The highly conserved untranslated regions of the hepatitis C virus (HCV) play a fundamental role in viral translation and replication and are therefore attractive targets for drug development A set of modified DNAzymes carrying (2′R)-, (2′S)-2′-deoxy-2′-C-methyl- and -2′-O-methylnucleosides at various positions of the catalytic core were assayed against the 5′-internal ribosome entry site element (5′-IRES) region of HCV Intracellular stability studies showed that the highest stabilization effects were obtained when the DNAzymes′ cores were jointly modified with 2′-C-methyl- and 2′-O-methylnucleosides, yielding an increase by up to fivefold in the total DNAzyme accumulation within the cell milieu within 48 h of transfection Different regions of the HCV IRES were explored with unmodified 10–23 DNAzymes for accessibility A subset of these positions was tested for DNAzyme activity using an HCV IRES-firefly luciferase translation-dependent RNA (IRES-FLuc) transcript, in the rabbit reticulocyte lysate system and in the Huh-7 human hepatocarcinoma cell line Inhibition of IRES-dependent translation by up to 65 % was observed for DNAzymes targeting its 285 position, and it was also shown that the modified DNAzymes are as active as the unmodified one
16 citations
27 May 2014
TL;DR: This paper aims to demonstrate the efforts towards in-situ applicability of EMMARM, which aims to provide real-time information about concrete mechanical properties such as E-modulus, compressive strength, and other properties related to E-commerce.
Abstract: Spanish Ministry of Economy and Competitiveness, No. BFU2012-31213; Junta de Andalucia, No. CVI-7430; and FEDER funds from the EU
6 citations
TL;DR: This work describes an original one-step multiplex reverse transcription polymerase chain reaction procedure, which allows testing the induction of interferon and proinflamatory related responses by nucleic acids in the cell system of choice.
3 citations
01 Jan 2014
TL;DR: This review provides an overview of those methodologies that have been mainly used for analyzing RNA folding and their application to the study of HCV molecular biology.
Abstract: RNA structure is used as a dynamic and robust supracoding system, beyond the nucleotidic sequence, to store critical information in a minimum size. The building blocks of this system are highly conserved folded genomic regions, the so-called functional RNA domains. They play, on their own, biological roles, such as interactions with proteins or nucleic acids. Therefore, deciphering the RNA structural code and understanding the structure-function relationship is critical for a deep knowledge of RNA function. This takes special relevance in the case of RNA viruses, which exhaustively make use of functional RNA domains to get replication efficient and compact genomes. The RNA genome of the hepatitis C virus (HCV) can be considered a prototype in the investigations about functional genomic regions. It contains multiple structurally conserved domains mostly located in the 5’and 3’-untranslated regions (5’UTR, 3’UTR). These elements participate in HCV translation and replication by recruiting viral and host protein factors and also by establishing a complex and active all-RNA interaction network. Long-range RNA-RNA contacts are related to conformational rearrangements at the 5’ end of the HCV genome and also to the structural transition in the 3’UTR from the replication-competent conformer to the dimerizable form. Together, the essentiality of functional RNA domains and their high conservation rate makes them potential therapeutic targets. This review provides an overview of those methodologies that have been mainly used for analyzing RNA folding and their application to the study of HCV molecular biology.