Hi,
In addition to what Dave mentioned, you could build a duplex and use
targeted MD to flip a base out of the helix.
I would recommend using this reaction coordinate:
http://pubs.acs.org/doi/pdf/10.1021/ct9001575
-Christina
On Tue, Apr 19, 2016 at 12:24 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Apr 19, 2016, giulia palermo wrote:
> >
> > I am trying to build a double stranded DNA with Nucleic acid builder
> > including an EXTRUDED guanine.
> > Is it possible to do it with NAB?
>
> It would not be easy with the building capabilities in NAB. I'd suggest
> finding an example of an extruded guanine in the PDB, and use that
> fragment to
> build what you want. The frames capability in NAB might be helpful, or you
> might just want to do it interactively in a visualization program.
>
> ...dac
>
>
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--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
http://home.chpc.utah.edu/~cheatham/
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Received on Tue Apr 19 2016 - 12:00:03 PDT
