1,721,018 research outputs found
Studies on the hydrolytic stability of 2?-fluoroarabinonucleic acid (2?F-ANA)
No full textThe stability of 2'-deoxy-2'-fluoroarabinonucleic acid (2'F-ANA) to hydrolysis under acidic and basic conditions was compared to that of DNA, RNA and 2'F-RNA. In enzyme-free simulated gastric fluid (pH approximately 1.2), 2'F-ANA was found to have dramatically increased stability (virtually no cleavage observed after 2 days) with respect to both DNA (t(1/2) approximately 2 min) and RNA (t(1/2) approximately 3 h (PO) or 3 days (PS)). These results were observed for both phosphodiester and phosphorothioate backbones and with multiple mixed-base sequences. Under basic conditions, 2'F-ANA also showed good stability. In 1 M NaOH at 65 degrees C, 2'F-ANA had a t(1/2) of approximately 20 h, while RNA was entirely degraded in a few minutes. Furthermore, the nuclease cleavage of phosphorothioate 2'F-ANA and DNA by snake venom phosphodiesterase was studied in detail. One diastereomer of the PS-2'F-ANA linkage was found to be much more vulnerable to enzymatic cleavage than the other, which is parallel to the properties observed for PS-DNA. Additional studies of 2'F-ANA-containing oligonucleotides are warranted based on the excellent stability properties described her
Chemically modified siRNA: tools and applications
No full textChemical modification provides solutions to many of the challenges facing siRNA therapeutics. This review examines the various siRNA modifications available, including every aspect of the RNA structure and siRNA duplex architecture. The applications of chemically modified siRNA are then examined, with a focus on specificity (elimination of immune effects and hybridization-dependent off-target effects) and delivery. We also discuss improvement of nuclease stability and potency
2?F-Arabinonucleic acids (2?F-ANA) — history, properties, and new frontiers
No full textThe development of arabinonucleosides and oligoarabinonucleotides is described, focusing especially on 2?-deoxy-2?-fluoroarabinonucleosides (araF-N) and -oligonucleotides (2'F-ANA). In addition to their chemical and enzymatic synthesis, we discuss various properties of 2?F-ANA: hydrolytic stability (to nucleases, acids, and bases), binding affinity to complementary strands, structure and conformation, and optimization of RNase H activity. We also discuss the use of 2?F-ANA in gene-silencing approaches (antisense, siRNA), and in the stabilization of higher-order structures (such as triplexes and quadruplexes) including aptamers. Finally, we examine several other oligonucleotide derivatives based on 2?F-ANA and look ahead to the future of 2?-fluoroarabinonucleosides and -oligonucleotid
Silencing disease genes in the laboratory and the clinic
No full textSynthetic nucleic acids are commonly used laboratory tools for modulating gene expression and have the potential to be widely used in the clinic. Progress towards nucleic acid drugs, however, has been slow and many challenges remain to be overcome before their full impact on patient care can be understood. Antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) are the two most widely used strategies for silencing gene expression. We first describe these two approaches and contrast their relative strengths and weaknesses for laboratory applications. We then review the choices faced during development of clinical candidates and the current state of clinical trials. Attitudes towards clinical development of nucleic acid silencing strategies have repeatedly swung from optimism to depression during the past 20 years. Our goal is to provide the information needed to design robust studies with oligonucleotides, making use of the strengths of each oligonucleotide technology
Nucleoside-tailored molecularly imprinted polymeric nanoparticles (MIP NPs)
Full text linkMIP NPs represent one of the current most suitable alternatives to antibodies for molecular recognition and diagnostic applications. Here we present the synthesis of MIP NPs imprinted for 2'-deoxyadenosine (dA) prepared using for the first time a modified polymerizable 2'-deoxyuridine complementary residue. We demonstrate that the introduction of this modified monomer results in an increase of the affinity of the produced MIP NPs, without altering their physical properties such as size, shape, or dispersibility. The imprinted NPs have shown the ability to specifically recognize dA, whereas no imprinting effect was observed for 2'-deoxyguanosine (dG) or deoxycytidine (dC). The results suggest that such monomers (and their phosphoramidites) could be used in the synthesis of oligomer or longer DNA sequences for potentially producing hybrid MIP–DNA materials with improved recognition performance
Chemical modification of siRNA
No full textThe ability to manipulate the RNA interference (RNAi) machinery to specifically silence the expression of target genes could be a powerful therapeutic strategy. Since the discovery that RNAi can be triggered in mammalian cells by short double-stranded RNAs (small interfering RNA, siRNA), there has been a tremendous push by researchers, from academia to big pharma, to move siRNAs into clinical application. The challenges facing siRNA therapeutics are significant. The inherent properties of siRNAs (polyanionic, vulnerable to nuclease cleavage) make clinical application difficult due to poor cellular uptake and rapid clearance. Side effects of siRNAs have also proven to be a further complication. Fortunately, numerous chemical modification strategies have been identified that allow many of these obstacles to be overcome. This unit will present an overview of (1) the chemical modifications available to the nucleic acid chemist for modifying siRNAs, (2) the application of chemical modifications to address specific therapeutic obstacles, and (3) the factors that must be considered when assessing the activity of modified siRNA
Effect of chemical modifications on modulation of gene expression by duplex antigene RNAs that are complementary to non-coding transcripts at gene promoters
No full textAntigene RNAs (agRNAs) are small RNA duplexes that target non-coding transcripts rather than mRNA and specifically suppress or activate gene expression in a sequence-dependent manner. For many applications in vivo, it is likely that agRNAs will require chemical modification. We have synthesized agRNAs that contain different classes of chemical modification and have tested their ability to modulate expression of the human progesterone receptor gene. We find that both silencing and activating agRNAs can retain activity after modification. Both guide and passenger strands can be modified and functional agRNAs can contain 2?F-RNA, 2?OMe-RNA, and locked nucleic acid substitutions, or combinations of multiple modifications. The mechanism of agRNA activity appears to be maintained after chemical modification: both native and modified agRNAs modulate recruitment of RNA polymerase II, have the same effect on promoter-derived antisense transcripts, and must be double-stranded. These data demonstrate that agRNA activity is compatible with a wide range of chemical modifications and may facilitate in vivo applications. <br/
Enhancer RNA facilitates NELF release from immediate early genes
No full textEnhancer RNAs (eRNAs) are a class of long noncoding RNAs (lncRNA) expressed from active enhancers, whose function and action mechanism are yet to be firmly established. Here we show that eRNAs facilitate the transition of paused RNA polymerase II (RNAPII) into productive elongation by acting as a decoy for the negative elongation factor (NELF) complex upon induction of immediate early genes (IEGs) in neurons. eRNAs are synthesized prior to the culmination of target gene transcription and interact with the NELF complex. Knockdown of eRNAs expressed at neuronal enhancers impairs transient release of NELF from the specific target promoters during transcriptional activation, coinciding with a decrease in target mRNA induction. The enhancer-promoter interaction was unaffected by eRNA knockdown. Instead, chromatin looping might enable eRNAs to act locally at a specific promoter. Our findings highlight the spatiotemporally regulated action mechanism of eRNAs during early transcriptional elongation
Partial Flipping To Support Learning in Lectures
No full textThis chapter outlines and expands on content presented at the Biennial Conference on Chemical Education in 2014. The use of the flipped classroom model to develop understanding and to enhance subsequent in-lecture learning is discussed, with a focus on supporting incoming students in adapting to the demands of studying at a research-intensive university in the UK. ‘Partial flipping’, whereby part of a lecture is made available in video form prior to the scheduled session, has been employed to free-up time in class for more effective learning activities. Two case studies are described, including evidence regarding student engagement and their response to the interventions. The second study involves interactive pre-lecture videos which feature multiple-choice and open-answer questions. The latter approach provides valuable learning analytics to support the integration of just-in-time support into the framework of a lecture in order to meet the needs of students effectively and provide targeted, timely feedback
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