DNA Structure prediction with a heteroatom !

[muthuscience]

Let me introduce myself as Muthukumaran doing my Masters in Indian Institute of Technology.
I'm currenlty interested to predict the 3 dimensional structure of double stranded DNA (30 mer). I
found your software 3DNA. Quite impressive. But, I'm interested to build the 3D structure of the
DNA with a heteroatom which is a dye in my case. Can 3DNA be used to accomplish
the task ? We have a NMR structure of the DNA with the dye but thats 20 mer. Is there a way to
cut n paste the dye to the predicted 30 mer from the NMR using any tool ? Thank you

[xiangjun]

Thanks for using 3DNA and your kind words about it.

But, I'm interested to build the 3D structure of the DNA with a heteroatom which is a dye in my case. Can 3DNA be used to accomplish the task ? We have a NMR structure of the DNA with the dye but thats 20 mer. Is there a way to cut n paste the dye to the predicted 30 mer from the NMR using any tool ?

If I understand it correctly/clearly, I do not think 3DNA can be applied directly for your purpose. However, if you are very specific as to what you have tried, what problem you have experienced and what you'd like to achieve, others and I may help you more concretely. For one thing, I am interested in expanding 3DNA's capability for model building.

Other tools you may try include coot and NAB -- I have not used either of them, but I have heard of them mentioned quite a bit.

Xiang-Jun

[temizna]

Assuming your 20mer and 30mer structures resemble average B-DNA conformation, you can build the 30mer using 3DNA. Then match 20mer NMR structure with the 30mer using VMD or UCSF Chimera. You can use the sugar phosphate backbone to rmsd match.

HTH,
Have fun!

Alpay

[muthuscience]

Thank you to both temizna and xiangjun. Will get back to you once I get a progress !