The power of RNA to regulate gene expression energizes the Schroeder lab. RNA, ribonucleic acid, folds into three-dimensional structures and thus achieves specificity in molecular recognition and enzymatic activity. Toward the long-term goal of RNA structure prediction from sequence, the Schroeder lab explores the structures of encapsidated satellite tobacco mosaic virus (STMV) RNA, the structures and energetics of prohead RNA (pRNA), and the thermodynamic stabilities of noncanonical pairs at RNA helix ends. None of these RNA structures are currently predicted well. Thus discovering new properties of these RNA structures and energetics will provide new insight into the fundamental physical forces that direct RNA folding and function. Additional experimental data about RNA conformations, such as chemical modification, phylogenetic covariation, improved thermodynamic parameters, and the magnesium dependence of RNA tertiary interactions, can further define the RNA conformational landscape and improve RNA structure predictions. Information from a variety of experiments including UV optical melting, NMR, crystallography, chemical probing, as well as standard molecular biology and biochemistry techniques, will be required to solve these problems. New computational tools are necessary to incorporate this new data into structure predictions. The lessons learned from solving these challenging problems will contribute to understanding the fundamental interactions that determine RNA structure and function and thus lead to better RNA structure predictions. Accurate RNA structure predictions can direct studies of RNA function and rational design of therapeutics that target viral RNA. Viruses, such as flu, HIV-1, hepatitis, and the common cold, have RNA genomes, and few remedies are available to treat these diseases. Many antibiotics target ribosomal RNA, and viral RNAs provide a gold mine of undeveloped therapeutic target sites
