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| Home > Publications database > Biophysical investigation of RNA folding: NMR-spectroscopic investigation of stem-loop 5 from SARS-CoV-2 |
| Home > Publications database > Biophysical investigation of RNA folding: NMR-spectroscopic investigation of stem-loop 5 from SARS-CoV-2 |
| Dissertation / PhD Thesis | PUBDB-2025-04082 |
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2025
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Please use a persistent id in citations: urn:nbn:de:hebis:30:3-920099 doi:10.3204/PUBDB-2025-04082
Abstract: When in 2020 the virus for the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) hitthe world, the response of the scientific community was tremendous. Scientists used not only state-of-the-art methodology but also reacted by developing effective countermeasures. Our group joined thisgoal with their expertise in nuclear magnetic resonance (NMR) spectroscopy. With our specialization inNMR of biomolecules like proteins and ribonucleic acids (RNAs) we coordinated a global network calledCOVID19-nmr (https://covid19-nmr.de). Substantial efforts in the Frankfurt team provided the basis forthe understanding of viral proteins and genomic RNAs. Other research groups identified viralcomponents of the SARS-CoV-2 coronavirus which allowed us to prioritize potential targets from anNMR and structural point of view. With our results, investigations were expanded: We screened viraltargets to libraries of low molecular weight ligands as start for medicinal chemistry campaigns.To study possible viral targets and the effects of pharmacological reagents the affected biologicalsystems and mechanisms need to be understood. The knowledge of a biological component, itsstructure and behavior, are key to the effective influence of cellular processes resulting from the viralinfection. In most cases, a reductionist approach is used to study the identified participants, as the overallview of the system can give the researcher an overwhelming amount of information that needs to bedeciphered. By changing the perspective and looking at the nature and behavior of individual systems,the information gain can be increased. The current research objective does not only benefit from theresults produced at present, but also from results achieved previously. Especially in case of the SARS-CoV-2 virus, the comparison to earlier known and human infecting coronaviruses provided a large poolof knowledge for scientific studies. However, the comparisons also showed that despite the previousknowledge, the data were not fully sufficient, leaving us with the possibility for vaccination but no curefor the coronavirus disease 2019 (COVID-19) caused by the virus. Therefore, research attempts tounderstand the virus and its constituents are of ongoing interest.In this work, I will present research results for structural investigation of the target RNA 5_SL5, which isthe 5th element of the 59-terminal untranslated region (UTR) of the SARS-CoV-2 viral genome. Due tothe location of the AUG start codon within the sequence it is the start side for the translation of the openreading frame (ORF) 1a/b, which encodes for 16 non-structural proteins (nsp) of the virus. Theinvestigation of the SL5 target was split due to its large sequence and structural fold. I will show thepossibility to investigate large RNA systems like this by the reductionism approach of divide-and-conquer. Several methods of structural and folding studies of RNA were used for an initial evaluation ofthe applicability of the divide-and-conquer approach, providing a comprehensive global view of thesystem. With this, the focus of this work were the designed sub-elements of the SL5 element and thepossibility to transfer insight gained from the individual sub-elements to the larger system. The methodNMR was extensively used to obtain a detailed chemical shift characterization of the sub-elements.Furthermore, NMR-experimental methods were used for the determination of individual base-pairstabilities as well as for the delineation of local dynamics. The impact of evolutionary changes(mutations) on the elements, hence by sequence alteration like those found in variants of concern (VoC),were investigated. In summary, the work is able to show the comparability of gathered information onthe small elements to the full-length system. It will also report on the difficulties arising when investigatinglarger RNA systems with NMR. Finally, a comparison of the combined structure-biological informationof the system will be presented.The investigations undertaken in this thesis are not able to clarify biological relevance or function on theSL5 within the virus machinery, but it gives detailed insight in an interesting target structure, which isconserved throughout the Coronaviridae. Therefore, this research provide an addition to the pool ofknowledge, which may drive future investigations.
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