Methylated DNA

Not exactly a Gromacs question, but is anyone aware of a tool that could generate a single-strand DNA structure containing a mix of methylated and unmethylated bases? I recall that CHARMM supports methylation, but is manually messing with existing non-methylated bases the only way?
Thanks!

Hi Sasha,

not the most elegant solution, but a shot - scripting the pymol building wizard might be something to try. I’m pasting a script for mutating an aminoacid using pymol here, you might be able to adapt it to nucleotide methylations.

from pymol import cmd
import sys

pdb, selection, mutant = sys.argv[-3:]
cmd.wizard("mutagenesis")
cmd.load("{}.pdb".format(pdb))
cmd.refresh_wizard()
cmd.get_wizard().set_mode(mutant)
cmd.refresh_wizard()
cmd.get_wizard().do_select(selection)
cmd.refresh_wizard()
cmd.get_wizard().apply()
cmd.refresh_wizard()
cmd.set_wizard()
print('--- SaVING now!')
cmd.save("{}_m.pdb".format(pdb), pdb)

Thanks for the suggestion. Problem is, unless I am missing something, pymol does not seem to be able to use the mutagenesis wizard on nucleotides. It really looks like we will need to script something from scratch. Definitely an idea for a tool, actually…

This can be done in a mostly automated way with CHARMM (software). The internal coordinate builder allows you to build any arbitrary molecule in any geometry, and you can apply methylation patches and other modifications to it.

Hey Justin,

Thanks. I’ve never used any of those tools, but looks like I may have to try.

Sasha