RNA Structure Characterization

Understanding the biological role of viral RNA is facilitated by knowledge of its higher order structure. Like cellular RNA, viral RNA can serve a variety of functional roles both as a coding and noncoding molecule. The primary structure of RNA—its nucleotide sequence—can fold itself into more complex secondary structures including hairpins/stem-loops, bulges, and pseudoknots. It’s these secondary structural elements that contribute to RNA's multifunctionality. One example is the hepatitis C virus 5' internal ribosomal entry site (IRES), whose complex RNA secondary structure serves as a docking site for ribosomal assembly to mediate cap-independent viral translation.

Emerging RNA structure-mapping technologies, which combine chemical probing with powerful bioinformatics, offer new means to explore structure-function relationships in biology, particularly in viral lifecycles. One such technique, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), exploits the inherent nucleophilicity of 2'-hydroxyls on RNA nucleotides that are in conformationally flexible positions. Chemical modification at these reactive sites provides information at single-nucleotide resolution of the RNA secondary structural environment. Recently, our laboratory demonstrated the ability of SHAPE to detect the binding of a small molecule inhibitor to the HCV 5' IRES which resulted in the loss of IRES structure and viral replication.

In this way, knowledge about RNA secondary structure not only provides insight to better understand virus biology, but it can also be used for the rational design of new therapeutics. Directly targeting viral RNA secondary structures for therapeutic purposes is a paradigm shift in both compound screening and drug design. 

Here we are currently developing highly potent and universal therapeutics against critical RNA secondary structures in Influenza viruses.