Fiber, analyze and rebuild in 3DNA

While browsing the current issue of Nucleic Acids Research (May 2009, Vol. 37, No. 8), I noticed, surprisingly, the article titled Reconstitution of ‘floral quartets’ in vitro involving class B and class E floral homeotic proteins by Rainer Melzer and Günter Theißen from Jena, Germany.

From the title and abstract, I would not expect 3DNA could play a role here. Yet in section Modeling a floral quartet, the authors used fiber to building a B-DNA model of floral quartets, using sequence between the XhoI and XbaI sites of probe A, then analyze the structure, and modified the resultant file 'bp_step.par' accordingly to their specifications, and rebuild a customized DNA model. In the following paragraph, the authors used the analyze/rebuild pair again for the CArG box bound to serum response factor.

This is the intended usage of the 3DNA software package I have had in mind from its initial design. I emphasized such versatile, integrated approach unique with 3DNA in our 2008 Nature Protocols paper. As time goes by, I am confident that more people will begin to appreciate this approach.