DNA 2 RNA structure

[biohegedus]

Hi,

I have a protein/DNA complex. I would like to substitute the DNA with RNA.
To see its rationality (e.g. clashes),, I would like to convert the DNA structure to RNA. I do not find any solution to add the oxygen to the sugar.
Can you suggest a tool or an approach? I have been working only with protein structures...

Thanks a lot in advance,
Tamas

[xiangjun]

Hi Tamas,

Thanks for posting your question on the 3DNA Forum. Unfortunately, 3DNA does not provide a straightforwad "solution to add oxygen to the sugar" to "substitute the DNA with RNA". Note that DNA is a protein-DNA complex is (most) likely in the B-form conformation, while RNA duplex is in A-form. Simply adding an 2'-oxygen to each sugar of a protein-DNA complex may not be meaningful.

Xiang-Jun