Hi,
This is a complicated segment of ssDNA to fold from an extended
conformation.
That being said, I'd suggest setting up Watson-Crick restraints on the
regions that are predicted to base pair. An example of how to do this can
be found in Tutorial A4.
http://ambermd.org/tutorials/advanced/tutorial4/
I'd be hesitant to trust results without some kind of experimental data to
compare to, though. Maybe truncating the system to a region of interest
would be more tractable as a test system? I don't know if there's any
structural information on this sequence in particular, but you could find
some on TATA hairpin motifs, non-canonical base pairs, and bulge regions
individually. Maybe you can validate your model based on these?
Hope this helps,
Christina
On Fri, Feb 20, 2015 at 6:46 AM, Urszula Uciechowska <
urszula.uciechowska.biotech.ug.edu.pl> wrote:
> I would like to also try the constraints in sander to fold the ssDNA.
> Which constraints should be the best for this case? I have attached the 2D
> ssDNA conformation that I would like to get.
>
> best regards
> Urszula
>
>
> > On Thu, Feb 12, 2015, Urszula Uciechowska wrote:
> >>
> >> I was wondering if its possible to build a ssDNA in hairpin conformation
> >> using nab? Does anyone know other software where I could do this?
> >
> > It is certainly *possible*: the pseudoknot example could be adapted to a
> > hairpin. It uses distance geometry to construct conformations satisfying
> > certain restraints, such as WC pairing in the stem.
> >
> > Having said that, there are lots of other solutions, and a Google search
> > will
> > point to many of them. I personally would use CYANA for this purpose,
> but
> > that is largely because I'm familiar with that code. You could also set
> > up
> > constraints in sander and "fold" the dna from an extended configuration.
> >
> > Maybe others on the list will have more specific suggestions.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> >
> >
>
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
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--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
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Received on Fri Feb 20 2015 - 07:00:04 PST
