Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
Fig 3
The display of typical predicted 3D structures, and comparisons of RMSDs between the present model and other models.
(A,C) The predicted 3D structures (ball-stick) with the mean (top) and minimum (bottom) RMSDs for (A) three sample dsDNAs (PDBs: 1agh, 1qsk, and 1mnm) and (C) three ssDNAs (PDBs: 4kbl, 2l5k, and 1jve) from their native structures (cartoon). (B,D) The comparison of the predicted structures between the present model and the existing models including the 3dRNA/DNA and the models from Scheraga’s or Saiz’s group for (B) 20 dsDNAs and (D) 20 ssDNAs. The results of 3dRNA/DNA are predicted through their online server based on the native secondary structures [53]. The other data is taken from refs. 56 and 59. The 3D structures are shown with PyMol (http://www.pymol.org).