Skip to main content
. Author manuscript; available in PMC: 2012 Jun 1.
Published in final edited form as: Methods. 2010 Dec 14;54(2):239–250. doi: 10.1016/j.ymeth.2010.12.010

Fig. 6.

Fig. 6

Plots of the RMSD values measured for the entire L-shaped monomer and its structure subsets relative to the starting state of the MD run of the full L-shaped monomer (tectosquare design LT17, monomer A3s). Shown in black are the RMSD values for the entire monomer (92nt), with the mean value of 6.11 ± 0.91 Å. Shown in red are the RMSD values of the helical arms and the connecting right angle junction (RA), a total of 62nt. Excluded are the 5′ and 3′ single strands and the hairpin loops. The mean RMSD value is 3.63 ± 0.90 Å. Thus the movements and distortions of the relatively short, disjoint, single-stranded elements excluded from consideration in the red plot contribute significantly to the full structure RMSD measure. Shown in blue are the RMSD values for the RA junction including the two proximal base pairs in each helical arm (total of 10nt), with the mean value of 1.03 ± 0.14 Å. The RA junction distortions measured in different ways (not shown) also show it to be the most stable subset of the entire L-shaped monomer.