Structural Energetics and Dynamics of Nucleic Acids and Their Interactions with Metal Ions
The second part of the thesis describes two investigations of Sarcin-Ricin Domain RNA: (1) characterization of the structural energetics and opening dynamics of individual bases and base pairs; (2) mapping divalent metal ion binding sites. Imino proton exchange measurements reveal that the structural stabilization free energies are broadly distributed in this RNA structure. One of the least stable sites is the noncanonical G-A base pair located next to the phosphodiester bond cleaved by alpha-sarcin. This finding supports the proposed base flipping mechanism for alpha-sarcin cleavage. Our results also indicate that the bases in the consensus loop have relatively long lifetimes in the open state. Mn2+ titration experiments demonstrate that of two specific Mn2+ ion binding sites exist in Sarcin-Ricin Domain RNA. One is located in the major groove of the stem part and the other one is located in the tetraloop.
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