NMR Structure and Dynamics and Computational Studies of RNA

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HallMCB 9816906Two RNA hairpins, the Iron Responsive RNA hairpin, with a six-nucleotide loop, and a UUCG tetraloop with either a C:G or G:C loop-closing base pair, are used here as model systems to probe structure, stability, and dynamics. The RNA structures are determined by 15N/13C/1H/31P heteronuclear NMR methods, and characterized thermodynamically using thermal melting monitored by ultraviolet absorption. 13C and 31P NMR relaxation measurements are used to determine the dynamics of the individual base and ribose, and phosphodiester backbone, respectively. To independently measure the dynamic motions of the RNA bases, 2-amino-purine is introduced at specific positions in the RNA, and the time-resolved fluorescence lifetimes and anisotropy are measured. These experimental results are compared with simulations of molecular structure and dynamics, using stochastic dynamics in a solvent continuum (GB/SA).The structure and flexibility of an RNA molecule will determine how it interacts with other cellular components, such as proteins or other nucleic acids. Several spectroscopic methods are now available to describe the structure and motional properties of small RNA molecules: nuclear magnetic resonance (NMR) provides structural information as well as a description of the flexibility of the structure, and fluorescence also provides a window on the time scales of the motion. These methods are applied to two RNA molecules which are anticipated to have distinctly different properties, reflecting their biological functions: one binds a protein, and the other acts as a staple to confine the structures of larger RNAs. Computational methods are then used to model their structures and intrinsic motions.