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@PHDTHESIS{Mertinkus:638475,
      author       = {Mertinkus, Klara Rebecca},
      othercontributors = {Schwalbe, Harald and Grininger, Martin},
      title        = {{B}iophysical investigation of {RNA} folding:
                      {NMR}-spectroscopic investigation of stem-loop 5 from
                      {SARS}-{C}o{V}-2},
      school       = {Johann Wolfgang-Goethe-Universität Frankfurt},
      type         = {Dissertation},
      reportid     = {PUBDB-2025-04082},
      pages        = {260},
      year         = {2025},
      note         = {Dissertation, Johann Wolfgang-Goethe-Universität
                      Frankfurt, 2025},
      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.},
      cin          = {EMBL-User},
      cid          = {I:(DE-H253)EMBL-User-20120814},
      pnm          = {6G3 - PETRA III (DESY) (POF4-6G3)},
      pid          = {G:(DE-HGF)POF4-6G3},
      experiment   = {EXP:(DE-H253)P-P12-20150101},
      typ          = {PUB:(DE-HGF)11},
      urn          = {urn:nbn:de:hebis:30:3-920099},
      doi          = {10.3204/PUBDB-2025-04082},
      url          = {https://bib-pubdb1.desy.de/record/638475},
}