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BP: Fachverband Biologische Physik
BP 15: Poster IIb
BP 15.28: Poster
Dienstag, 19. März 2024, 18:00–20:30, Poster F
Structural motif stability of bacteriophage MS2 RNA packaging signals upon changes in their flanking sequence — •Veronika Bukina1,2 and Anže Božič1 — 1Jožef Stefan Institute, Ljubljana, Slovenia — 2University of Ljubljana, Slovenia
The RNA motifs can be responsible for specific important functions. For instance, in bacteriophage MS2, they serve as packaging signals (PSs), which play a crucial role in binding viral coat proteins during capsid assembly. This work aims to analyze motif structural stability on the example of the well-studied MS2 virus. As a consequence of current experimental studies, which reveal the multiple putative PS sites across the MS2 RNA genome, we focus on 14 RNA motifs of the virus, including the most widely known TR hairpin. The study of motif stability involves manipulating the flanking sequences surrounding them and comparing various measures calculated from their secondary structure, such as structure probability, ensemble defect, and Shannon entropy. To verify the tertiary structures of these RNA segments, the oxDNA software is employed. Our results show the stability of certain motifs regardless of the presence or absence of sequences around them, even when the nucleotide content of flanking sequences is randomized. Conversely, other unstable motifs are stabilized by genome or flanking sequences that tell us about the importance of the particular structure as well as of the genome sequence. The outcome of this work is beyond viral PS structural stability, extending to applications in RNA binding protein (RBP) studies and more.
Keywords: RNA; motif stability; secondary structure; thermodynamics; MC