On Fri, Nov 09, 2012, Souvik Sur wrote:
>
> How can I make quadruplex structure from a 31 mer single strand oligomer
> ? Is there any tutorial for quadruplex formation in amber module, please
> suggest me.
You *could* try to build the quadruplex using the distance geometry mechanism,
in a way similar to how an RNA pseudoknot is built (see the Distance Geometry
chapter). But if you know what kind of quadruplex you have, you probably
would have better luck starting from a known structure, then modifiying
the bases to match the sequence you want.
For the latter, Google on "quadruplex model builder dna", and the top hit will
be a 2010 chapter by Haider and Neidle that goes into some detail about how
they attack this problem. Prof. Cheatham has also done recent work in this
area: check out http://home.chpc.utah.edu/~cheatham/index.html.
...dac
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Received on Fri Nov 09 2012 - 18:00:03 PST
