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. Author manuscript; available in PMC: 2017 Sep 1.
Published in final edited form as: Methods Enzymol. 2015 Feb 3;553:235–258. doi: 10.1016/bs.mie.2014.10.062

Figure 2.

Figure 2

(A) The data for the dynamics of water HBs (left) and Na+ (right) with base, ribose, and base (left) are described by the appropriate autocorrelation functions. (B) Temperature dependence of water HB relaxation time of bulk water and around four nucleotides, 24U, 29A, 33C, and 35A or PreQ1. Arrhenius fits are made to T > 200 K for the four nucleotide and bulk water. Alternatively, the relaxation dynamics of bulk water HB can be fit using the Vogel–Fulcher–Tamman (VFT) equation over the full range of temperatures (dashed line) (Yoon et al., 2014). (C) Water dynamics induced fluctuations of a base pair. The status of base pair (N1A3–N3U24), quantified by calculating logistic function φ(r) = (1 + e(r−r0)/σ)−1 as well as distance r, shows apparent fluctuations, whose time scale is ~10 ns. Figures adapted from Yoon et al. (2014, 2013).