Conceptualizing Ribosomal mRNA Unwinding Utilizing DMS MaP-Seq

Examining the dynamicity of RNA structure has deepened our understanding of its vast biological functions. Perhaps the protein complex that encounters the most diverse landscape of RNA structure is the ribosome. In translation, the ribosome must linearize countless mRNA conformations for proper protein production. Some RNA structures, however, reliably make up sequences which hinder the ability of the ribosome to maintain its reading frame. Arguably, the most well-studied of these structures is the RNA pseudoknot. Here, we present an approach utilizing dimethyl sulfate probing with mutational profiling and sequencing (DMS MaP-Seq) to precisely examine RNA unwinding. DMS MaP-Seq is a method typically used in predicting RNA secondary structure. Instead, we employ the method to understand the unfolding of the Sugarcane Yellow Leaf Virus pseudoknot (ScYLV _PK ). We demonstrate that the unwinding of ScYLV _PK is inherently different with regards to the ribosome and temperature. Additionally, we find that minor-groove triplex interactions support coaxial stacking, providing a major source of stability to ScYLV _PK in ribosomal unwinding.