The ultimate goal of this research is to characterize the forces directing RNA folding, and to use this knowledge to reliably predict structures of RNA molecules from their sequences. Since most diseases are mediated through RNA, and some viruses, including AIDS, are RNA, the results can lead to rational design of drugs. The results should also further the interpretation of sequences determined by the Human Genome Project. The foundation for structure prediction will be provided by studies of the thermodynamic and structural properties of oligonucleotides. Our understanding of the principles governing RNA folding will be tested by comparing predicted and known secondary structures. Studies of substrate binding and dynamics on a group I ribozyme will begin to provide insight into tertiary interactions important for RNA folding.

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National Institute of General Medical Sciences (NIGMS)
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Molecular and Cellular Biophysics Study Section (BBCA)
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University of Rochester
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Berger, Kyle D; Kennedy, Scott D; Schroeder, Susan J et al. (2018) Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops. Biochemistry 57:2121-2131
Smith, Louis G; Zhao, Jianbo; Mathews, David H et al. (2017) Physics-based all-atom modeling of RNA energetics and structure. Wiley Interdiscip Rev RNA 8:
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Kauffmann, Andrew D; Kennedy, Scott D; Zhao, Jianbo et al. (2017) Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions. Biochemistry 56:3733-3744
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