RNA motifs can be responsible for specific important functions. 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 viral RNA genome. The results indicate the stability of certain motifs regardless of the presence or absence of sequences around them. 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.
