Single Strand DNA (ssDNA) 3D structure prediction

[Anonymous]

I have an ssDNA and want to predict its 3D structure. Can I use Rosetta?
The secondary structure of my sequence is attached. For RNA we can use Rosetta to predict 3D structure but unfortunately I could not find any tools that predict tertiary structure of ssDNA? Please guide me, can i simply change Ts to Us, and predict a 3D RNA structure using Rosetta etc and finally in 3D structure replace Us with Ts?

Thank you very much.

[Anonymous]

*Can* you do that, yes. *Should* you do that, probably not. Rosetta doesn’t have any scorefunctions for single stranded DNA, and the RNA scorefunctions probably contain assumptions related to the extra flexibility of RNA over DNA. It’s worth trying, but the results may not be terribly reliable.

[Anonymous]

Thank you very much, Is there any other software that have score functions for ssDNA?

[Anonymous]

::shrug:: Try pubmed.

[Anonymous]

I got some tips from Phil Bradley:

I’m not aware of any functionality in Rosetta for predicting unbound DNA structure. There is some work from Honig and Rohs on MC modeling of DNA structure, that might be one place to look. Also these two web servers can generate models of DNA:

http://structure.usc.edu/make-na/server.html

http://haddock.chem.uu.nl/dna/dna.php

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