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- Wacker, A, et al.
(author)
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Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
- 2020
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In: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 48:22, s. 12415-12435
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Journal article (peer-reviewed)abstract
- The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5′ end, the ribosomal frameshift segment and the 3′-untranslated region (3′-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
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| 3. |
- Banijamali, S. M., et al.
(author)
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Effect of Ce Addition on the Tribological Behavior of ZK60 Mg-Alloy
- 2021
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In: Metals and Materials International. - : Springer. - 1598-9623 .- 2005-4149. ; 27:8, s. 2732-2742
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Journal article (peer-reviewed)abstract
- The present work aims to study the tribological behavior of an extruded ZK60 alloy in the presence of Ce; in a previous study, among ZK60 alloys with different Ce addition rates, an alloy with 3 wt% of Ce was found to exhibit the most promising mechanical (e.g., hardness and strengths) properties, while its wear behavior remained unknown. The results of microstructural examinations by optical and electron microscopes show that Ce addition reduces the grain size from 6.1 to 2.0 μm. Besides, in addition to the precipitates already distributed in the base alloy (Mg7Zn3), Ce could promote the formation of a new precipitate (MgZn2Ce), increasing the total fraction of the precipitates. These microstructural evolutions enhance the strengths of the studied ZK60 alloy, as the yield and tensile strengths increase from 212 to 308 MPa and from 297 to 354 MPa, respectively. A pin on disc tribometer was employed to study the wear behavior of the developed alloy under different normal loads (5, 20, 40, and 60 N). The results show that the base and Ce-added alloys exhibit almost a similar frictional behavior, while the wear resistance of the Ce-added alloy is higher within the load ranges applied: (i) in low load conditions (5 and 20 N), where the abrasive wear is the active mechanism, the precipitates in the Ce-added alloy could enhance the wear resistance. (ii) Under the load of 40 N, oxidative wear is also an operative wear mechanism, leading to a sharp increase in the wear rate of the alloys. In this condition, Ce could provide a protective oxide layer, which could improve the wear resistance of the alloy. (iii) At a load of 60 N, both studied alloys exhibit a similar wear rate due to a severe oxidation condition. Therefore, beyond this loading condition, the microstructural evolutions (e.g., change in precipitation behavior) caused by Ce addition can no longer contribute to the enhancement of wear resistance.
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| 4. |
- Schnieders, R, et al.
(author)
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1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5'-UTR of SARS-CoV-2
- 2021
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In: Biomolecular NMR assignments. - : Springer Science and Business Media LLC. - 1874-270X .- 1874-2718. ; 15:1, s. 203-211
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Journal article (peer-reviewed)abstract
- The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5′- and 3′-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5′-untranslated region (5′-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5′-UUUCGU-3′ hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive 1H, 13C and 15N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.
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| 6. |
- Kosek, David M, et al.
(author)
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Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility
- 2023
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In: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 51:20, s. 11162-11177
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Journal article (peer-reviewed)abstract
- MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression by binding to specific sites in mRNAs. Site recognition is primarily mediated by the seed region (nucleotides g2–g8 in the miRNA), but pairing beyond the seed (3′-pairing) is important for some miRNA:target interactions. Here, we use SHAPE, luciferase reporter assays and transcriptomics analyses to study the combined effect of 3′-pairing and secondary structures in mRNAs on repression efficiency. Using the interaction between miR-34a and its SIRT1 binding site as a model, we provide structural and functional evidence that 3′-pairing can compensate for low seed-binding site accessibility, enabling repression of sites that would otherwise be ineffective. We show that miRNA 3′-pairing regions can productively base-pair with nucleotides far upstream of the seed-binding site and that both hairpins and unstructured bulges within the target site are tolerated. We use SHAPE to show that sequences that overcome inaccessible seed-binding sites by strong 3′-pairing adopt the predicted structures and corroborate the model using luciferase assays and high-throughput modelling of 8177 3′-UTR targets for six miRNAs. Finally, we demonstrate that PHB2, a target of miR-141, is an inaccessible target rescued by efficient 3′-pairing. We propose that these results could refine predictions of effective target sites.
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