Collaborative Research: Probing the role of chemical modifications on structure, folding, and dynamics of tRNA isodecoders

With this award, the Chemistry of Life Processes program in the Division of Chemistry supports Drs. Harish Vashisth from the University of New Hampshire and Esteban A Orellana Vinueza from Dartmouth College to study how modifications to nucleic acid bases affects the structure of tRNAs and their functions in the biosynthesis of proteins. Transfer RNA (tRNA) delivers amino acids to ribosomes for the construction of proteins, with the three-base anticodon of tRNA specifying which amino acid is brought to the ribosome. The sequence of nucleotides outside of the anticodon can vary to create what are known as isodecoders of the tRNA. The nucleotide bases of isodecoders are chemically modified by cells under environmental changes, at different stages of cellular development developmental stages, and between cell types. This project applies approaches from the disciplines of biological chemistry as well as theoretical and computational chemistry to enhance the understanding of how these modifications affect the structures, dynamics, and folding/misfolding mechanics of the tRNA isodecoders, and reveals their potential roles as therapeutic targets and diagnostic biomarkers. This project is integrated into outreach and broader impact activities that visually teaches spatial thinking skills about RNA structure and function to STEM learners. The result is to increase the national talent pool for the STEM workforce in the emerging areas of RNA-based chemical tools and technologies. This research project addresses fundamental questions about the structures of tRNA isodecoder molecules and studies the impact of chemical modifications to uniquely alter tRNA structures and folding mechanisms. A combination of experimental techniques (spectroscopic methods, CRISPR technology, translation assays, and proteomics) and computational techniques (molecular dynamics simulations and thermodynamic property calculations) are used to resolve the functional, conformational, and energetic effects of chemical modifications in tRNA isodecoders. The project also establishes approaches, including new protocols for computing circular dichroism spectra of RNA molecules based on conformational ensembles from atomistic simulations, that are broadly applicable to other RNA molecules. Moreover, the conformational and thermodynamic property datasets emerging from simulations are highly useful in training of data-driven learning models. The education and outreach broader impact activities contribute to implementation of the next-generation science standards, increase in national talent pool, and enhanced education about RNA based technologies through summer research programs, 3D printing based and software generated molecular models, seminar series, journal clubs, and course teachings. 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.