Salt dependence of RNA collapse transition
Gokhan Caliskan 1,2, Robert Briber 3, Ursula Perez-Salas 2, Deverajan Thirumalai 4, Sarah Woodson 1
1 T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD
2 NCNR, NIST, Gaithersburg, MD
3 Dept. of Materials Science and Engineering University of Maryland, College Park, MD
4 Institute For Physical Science and Technology, University of Maryland, College Park, MD
Certain RNA molecules need to adopt a three dimensional compact state in order to function. Unlike proteins, which are driven to their globular states by hydrophobic interactions, RNAs undergo a cationic condensation to reach their globular state. Cations screen the repulsion between the negatively charged phosphates on the RNA backbone, the extended chain collapses first into a disordered intermediate state, and later the native interactions are established in a longer time scale. It is crucial to understand the mechanism of the collapse transition in order to elucidate the formation of the final native interactions.
We have run Small-Angle X-Ray Scattering (SAXS) experiments on Azoarcus ribozyme solutions in order to understand the salt dependence of the collapse transition. Titrations in NaCl, MgCl2, CaCl2 and Co(NH3)6 have shown that the transition strongly depends on the type and valence of the cation used. Higher valence in the cation leads the transition to take place at lower charge concentrations. Our results point that there should be multiple competing effects that play a role in the collapse transition. In addition to electrostatic forces, entropy of the loosely bound cations might influence the collapse transition.
Our preliminary SAXS measurements on a larger momentum transfer scale give some structural information about the different states of the RNA. We also explore the possibility of getting more detailed information about different solution states with computer simulations.
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Category: Biology and Biotechnology