CAREER: Shape-based differentiation of RNA elements using small molecules

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With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Professor Amanda Hargrove of Duke University to investigate critical differences in the shape of regulatory RNA structures through the development of novel technologies. The central dogma of molecular biology has long stated that DNA codes for RNA, which codes for protein, which then carries out a cell's important functions; but there is a rapidly growing appreciation for the functions of RNA itself in fundamental biology. At the same time, there is a pressing need for new techniques to investigate these functions, including how RNA interacts with other molecules. In this work, Hargrove and coworkers develop new technology to meet this need using pattern-based recognition, which is similar to human's sense of taste, wherein a handful of receptors can identify a wide range of flavors based on how the components of those flavors differentially interact with the receptors. In this application, small organic molecules are used as receptors to evaluate different "flavors" of RNA structure and rapidly reveal how the shape of RNA corresponds to its function. The assay developed will be widely accessible for future investigations into the classification of RNA functional motifs, and the library of small molecule receptors and their properties will be a publicly available and searchable database. The knowledge and technology produced provide the basis for novel, fundamental discoveries into the structure and function of regulatory RNAs and thus, the central dogma of molecular biology, which impacts all areas of life, from the environment to human health. These innovative technologies push the limits of differential sensing to include structural biology, paving the way for the structure-based classification of additional biomacromolecules. This research integrates with the educational plans of the PI to: 1) implement research-based experiments and collaborative projects among diverse undergraduate and high school students throughout North Carolina; 2) increase student understanding of noncovalent interactions via accessible visualization and application activities; 3) introduce students to interdisciplinary research and real-world applications of chemistry and chemical biology; and 4) increase student engagement in the study of STEM fields. The long-term research goal of the PI is to establish guiding principles for small molecule and protein recognition of RNA and to use these principles for the development of chemical probes for RNA structure and function. The CAREER research objective is to draw upon exquisitely tunable small molecules to develop timesaving and simple technologies that elucidate critical principles in RNA recognition and related function. The identification of functional yet non-protein coding RNA (ncRNA) sequences has led to a revolution in molecular biology, yet myriad questions surround the molecular function of ncRNA. These knowledge gaps include the driving principles behind ncRNA molecular interactions, particularly the influence of three-dimensional shape, and how these interactions guide ncRNA-dependent processes. Fundamental investigations of ncRNA biochemistry are hindered by challenges in molecular characterization, including the intensive time and expertise required to determine 3D RNA structure. Using techniques recently developed in the lab of the PI, the proposed work addresses a number of fundamental molecular questions, including: 1) How does shape influence small molecule:RNA recognition? 2) What RNA structural elements can small molecule receptors differentiate? 3) How do varying environmental conditions impact this differentiation? 4) How do base modifications influence RNA recognition? 5) Can arrays of small molecules differentiate functional RNA elements in a manner comparable to or better than proteins? These novel, small molecule-based methods for understanding RNA recognition provide ready access to chemical insights that reveal both the fundamental principles of small molecule:RNA recognition and the pivotal role RNA shape plays in regulating key cellular functions, ultimately leading to new knowledge in the ncRNA field.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.