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Author Topic: How do I build nucleic acid structures with sugar-phosphate backbone?  (Read 5215 times)

Offline xiangjun

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The easiest way to build a nucleic acid structure with the sugar-phosphate backbone, other than predefined fiber models, is to use the rebuild program. The backbone building scheme uses exactly the same protocol as the default for base-only model. The user needs to add the -atomic option to rebuild, and to choose the desired rigid sugar-phosphate backbone to be attached to the standard base geometry.

The four types of currently available backbone conformations are listed in the directory $X3DNA/config/atomic. To use any of these backbones, it is necessary to copy the standard nucleotide files associated with each type of backbone to $X3DNA/config or your current working directory, and to name each nucleotide as follows: Atomic_X.pdb (where X = A, C, G, T, U; or Atomic.x.pdb where x =  a, c, g, t, u for modified bases). The default Atomic_X.pdb files contains only the C1' backbone atom, and the base geometry is independent of the backbone conformation.

To build a DNA structure with B-DNA backbone conformation, for example, one uses the BDNA_X.pdb set to replace Atomic_X.pdb. There is a sub-command cp_std of the Ruby utility program x3dna_utils to help with this: x3dna_utils cp_std BDNA. This will copy BDNA_X.pdb to the current working directory and rename it Atomic_X.pdb. Please note that rebuild searches for Atomic_X.pdb files first in the current working directory, and then in $X3DNA/config.

To make the above description clear, here is an example. Go to the directory $X3DNA/examples/analyze_rebuild, and try to reproduce the following:
  • use the command, x3dna_utils cp_std BDNA, so that you will have Atomic_X.pdb files
  • use find_pair bdl084.pdb stdout | analyze stdin, to analyze the structure bdl084 (355d) and to generate a file named bp_step.par
  • use rebuild -atomic bp_step.par bdl084_3dna.pdb, to generate the PDB file bdl084_3dna.pdb with a standard B-backbone
The RMSD between all atoms of the original bdl084.pdb file and the generated bdl084_3dna.pdb file is only 0.73 Å. Please note that in the rebuilt bdl084_3dna.pdb file, some O3'(i-1) to P(i) linkages can be quite long (broken). This structure, however, serves well as a starting point for further energy minimization. See post "Restraint optimization of DNA backbone geometry using PHENIX" for how to regularize the overlong bonds.
« Last Edit: September 07, 2013, 08:23:23 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]


Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.