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. 2015 Sep;21(9):1578–1590. doi: 10.1261/rna.051102.115

FIGURE 1.

FIGURE 1.

Images of RNA systems simulated in this study include (A) the r(CCCC) tetranucleotide, shown in an A-form conformation with bases colored by residue number, (B) the r(GACC) tetranucleotide, shown in the NMR major conformation with bases colored by residue number, (C) the r(GGCAC-UUCG-GUGCC) 2KOC NMR ensemble, where the A:U base pair is shown in green, G:C base pairs are shown in light blue, and the UUCG loop sequence is shown in dark blue, (D) r(CAC-UUCG-GUG), a truncated version of structure 1 from the 2KOC NMR ensemble, used as a starting structure for M-REMD simulations, and (E) The UUCG tetraloop with alternate stem sequence, used as a starting structure for Anton simulations. The G:C base pairs are shown in light blue and the UUCG loop sequence in dark blue. We note that an alternative stem structure was used in the Anton simulations (in the 2010–2011 timeframe) to be consistent with our earlier tetraloop investigations. In this earlier study, representatives of all tetraloop structures found in the PDB were grafted onto a common stem structure; these relatively short MD simulations with even more poorly performing force fields were never published.