COMP 216 |
| The polyelectrolyte behavior of a RNA three-way junction is studied in the presence of monovalent and divalent cations. We predict the salt dependence of folding and opening rates of 16S rRNA three-helix junction as a function of Mg2+ and Na+ concentrations. The results are in rather good agreement with experimental data of transition rates between open and folded conformations of the 16S rRNA junction using fluorescence correlation spectroscopy and FRET on immobilized single molecules (collaboration with A. Spasic, Boston College; S. Chu, Stanford University and Berkeley). We will also discuss compact folding in randomly generated RNA sequences that were of sufficient length and information content to encode complex, functional folds, yet were unbiased by either genealogical or functional constraints (collaboration with David Bartel and E. Schultes, MIT). The unevolved, nonfunctional RNAs typically acquired magnesium-dependent folding states as compact as those of evolved RNA isolates. This work was supported by NSF. |
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Protein-Nucleic Acid Interactions: Experimental and Modeling Analysis
8:00 AM-12:15 PM, Tuesday, August 21, 2007 BCEC -- 156B, Oral
Division of Computers in Chemistry |