Abstract
Functional non-coding RNA molecules must assume a specific tertiary structure in order to properly catalyze important reactions in vivo. Due to the intrinsic negative charge of RNA, this folding process is inherently dependent on the interplay between the RNA molecule itself and its surrounding positive counterions which neutralize the overall charge and allow for stabilization of the RNA tertiary structure. We present here a novel algorithmic approach to calculating the divalent-ion mediated free energy of an RNA conformation based on established theory that considers the ions explicitly. By efficiently searching the local energy landscape, the free energy of the system can be evaluated quickly and directly. The speed and accuracy of this direct approach allows for simple integration into preexisting all-atom RNA simulation with which we demonstrate ion-mediated effects on the P4-P6 domain of the Tetrahymena Group I Intron.
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