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  • Journal article

  • TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets

    • Authors : Neugroschl, Atara  (2023)

  • Nucleic acid probes are valuable tools in biology and chemistry and are indispensable for PCR amplification of DNA, RNA quantification and visualization, and downregulation of gene expression. Recently, triplex forming oligonucleotides (TFO) have received increased attention due to their improved selectivity and sensitivity in recognizing purine-rich double-stranded RNA regions at physiological pH by incorporating backbone and base modifications. For example, triplex forming pep...
  • Journal article

  • Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins

    • Authors : Cannon, Kevin S. (2023)

  • processes such as signal transduction, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported highresolution stru...
  • Journal article

  • Antisense pairing and SNORD13 structure guide RNA cytidine acetylation

    • Authors : Gamage, Supuni Thalalla (2023)

  • N4-acetylcytidine (ac4C) is an RNA nucleobase found in all domains of life. Establishment of ac4C in helix 45 (h45) of human 18S ribosomal RNA (rRNA) requires the combined activity of the acetyltransferase NAT10 and the box C/D snoRNA SNORD13. However, the molecular mechanisms governing RNA-guided nucleobase acetylation in humans remain unexplored. Here we report two assays that enable the study of SNORD13-dependent RNA acetylation in human cells. F...
  • Journal article

  • Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

    • Authors : Yadav, Ruchi (2023)

  • SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 34 pandemic. Its ~30 kb RNA genome is translated into two large polyproteins subsequently cleaved 35 by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential 36 yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11 37 polyprotein, whose mature products are cofactors of the viral replicase, identifying the&#...
  • Journal article

  • Structural Insights into the Iron Nitrogenase Complex

    • Authors : Schmidt, Frederik V.  (2023)

  • Nitrogenases are best known for catalysing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO2) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the nitrogenase family the iron nitrogenase is the isozyme with the highest wildtype activity for the reduction of CO2, but the molecular architecture facilitating these&#...
  • Journal article

  • Considerations on activity determinants of fungal polyphenol oxidases based on mutational and structural studies

    • Authors : Nikolaivits, Efstratios (2021)

  • Polyphenol oxidases (PPOs) are an industrially relevant family of enzymes, being involved in the post-harvest browning of fruits and vegetables, as well as in human melanogenesis. Their involvement lies in their ability to oxidize phenolic or polyphenolic compounds, that subsequently form pigments. PPO family includes tyrosinases and catechol oxidases, which in spite of their high structural similarity, exhibit different catalytic activities. Long-standing research efforts&...
  • Journal article

  • Nanopore dwell time analysis permits sequencing and conformational assignment of pseudouridine in SARS-CoV-2

    • Authors : Fleming, Aaron M. (2021)

  • Nanopore devices can directly sequence RNA, and the method has the potential to determine locations of epitranscriptomic modifications that have grown in significance because of their roles in cell regulation and stress response. Pseudouridine (Ψ), the most common modification in RNA, was sequenced with a nanopore system using a protein sensor with a helicase brake in synthetic RNAs with 100% modification at 18 known human pseudouridinylati...