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. Author manuscript; available in PMC: 2013 Jun 7.
Published in final edited form as: J Am Chem Soc. 2012 Jul 16;134(29):12043–12053. doi: 10.1021/ja301454u

Figure 2.

Figure 2

Mg2+ affects RNA kinetics. (a) The distribution of autocorrelation times (ACT) for the MD trajectories projected onto the lowest 50 normal modes. The time scales of RNA fluctuations increase with Mg2+ concentration in accordance with experiment. This occurs because Mg2+ tightens RNA tertiary contacts and stabilizes compact conformations. (b) The distribution of autocorrelation times for the local Mg2+ density around several association sites. The time scales of RNA fluctuations are comparable to the time scale of the RNA fluctuations, which allows them to kinetically couple. (c) The residence time for the association sites.