Grant: Discovery Grants Program - Individual

Modifications on RNA and DNA can have profound effects on their structure, stability, biomolecular interactions, and cellular fate. My research and training program focuses on developing technologies to install, sequence, and study the impact of modifications in synthetic and naturally occurring RNA and DNA. Building from our preliminary studies this proposed program will focus on three major thrusts: 1) Methods to generate and evolve highly modified nucleic acid polymers Single-stranded DNA (ssDNA) can be evolved to bind molecular targets. However, its deficit of chemical diversity limits its functional potential. The first thrust of this proposed program is the development of methods to generate ssDNA with increased chemical diversity so that they may be evolved with improved binding properties and nuclease resistance. This thrust will impact the Canadian health sector by providing critically needed affinity reagents for applications ranging from disease diagnostics to therapeutics, while also providing antibody mimetics for fundamental research in biology. 2) Methods to sequence the epitranscriptome RNA modifications, collectively referred to as the epitranscriptome, have profound effects on the fate and function of RNA. Not surprisingly, their dysregulation has been implicated in numerous diseases, particular cancer. With over 170 known RNA modifications, deciphering their biological roles remains an unmet challenge. To date, only a fraction of the vast epitranscriptome has been mapped due to the lack of sequencing methods for individual modification types. In this thrust, we will develop chemistry-based sequencing methods for new and under-explored RNA modifications. This thrust will provide highly enabling tools for biologists to study RNA modifications and begin to unravel this burgeoning paradigm of gene regulation and its impact on human health. 3) Methods to identify positive allosteric modulators of RNA-binding proteins RNA modifications can be specifically recognized by epitranscriptomic reader proteins (ERPs), which is crucial to the regulation of RNA. These ERPs have only recently come to light as a key area of RNA biology. Chemical probes that modulate these protein-RNA interactions are essential to fundamental biological studies. Positive allosteric modulators (PAMs) are molecules that bind allosteric sites of a receptor resulting in a shift to its active state; within the context of ERPs, PAMs would increase affinity of the protein for its RNA target. Building from our expertise with DNA-encoded libraries (DELs), we will develop a method to identify PAMs from DEL screens by utilizing principles of cooperative multivalency. This thrust will greatly accelerate the discovery of PAMs, which are critically needed across the biological sciences to test fundamental hypotheses of protein function, while also directly impacting drug discovery programs targeting proteins with lower activity or expression levels in disease states.