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. 2004 Dec 1;32(21):6304–6311. doi: 10.1093/nar/gkh971

Figure 3.

Figure 3

Atomic root-mean-square fluctuation (Rmsf) (heavy atoms of RNA) observed during the MD simulations versus heavy atom number. The atom numbers follow the order phosphate, sugar and base of each nucleotide from 5′ to 3′ end. The second strand starts in the middle of each panel. The black curves indicate the atomic fluctuations of the 5′-rCGUUACG/5′-rCGUAACG duplex (A), the 5′-rCGCFGCG/5′-rCGCAGCG duplex (B), the 5′-rCGCPGCG/5′-rCGCAGCG duplex (C), the 5′-rCGCFGCG/5′-rCGCFGCG duplex (D) and the 5′-rCGUFACG/5′-rCGUAACG duplex (E), respectively. For comparison, the atomic fluctuations of the 5′-rCGCUGCG/5′-rCGCAGCG duplex are shown as grey dashed line in each panel.