Kari Pederson - Unifying Solution and Solid-State NMR Studies of Nucleic Acid Dynamics

Document created by Kari Pederson on Aug 22, 2014
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  Pederson, K.; Echodu, D.; Emani, P.; Olsen, G.; Bardaro, M. F.   J.; Shajani, Z.; Meints, G.; Miller, P.; Varani, G.; Drobny, G.   P. In Encyclopedia of Magnetic Resonance 2010.


  The last few years have seen a remarkable increase in interest in   the role of protein motion in catalysis, the energetics of   protein folding and molecular recognition. While motion and   conformational adaptation is also very important for nucleic   acids (many RNAs and DNAs function by undergoing large   conformational changes in response to binding of a protein or   small molecule), it is still not clear how motion contributes to   the function of nucleic acids. There is a clear need to study   motions and conformational transitions of nucleic acids by   applying biophysical techniques that extend the description of   DNA and RNA beyond the familiar static structures. It is well   known that different dynamic spectroscopies display variable   sensitivity to different rates of motion; therefore, to rely upon   any single type of spectroscopic measurement runs the risk of   obtaining either an incomplete or incorrect description of   internal molecular motions. Here we use solution and solid-state   NMR to study the dynamics for two paradigmatic nucleic acid   systems whose biological function depends on their ability to   change structure: the flipping out of a deoxycytidine by the   HhaI methyltransferase and TAR RNA which must undergo a   structural rearrangement of its bulged loop to bind to the tat   protein.  In both cases, structures in the absence and   presence of ligand are well described. Yet, little experimental   data exists to define over the dynamic pathways linking these   states, and how they depend on sequence. In both cases we use   solid-state 2H NMR line shapes to probe for the   presence of internal motions in the ms-ns timescales and   relaxation to investigate dynamics at ns and shorter. We show   that solid-state NMR can quantify motions at time scales not   easily probed by solution NMR relaxation techniques and we show   that solution and solid-state NMR views of the internal and   overall rotations of these molecules can produce a unified view   of the dynamics of these biomolecular systems.

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