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Questions and answers => General discussions (Q&As) => Topic started by: biohegedus on September 01, 2014, 04:42:08 am

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Title: DNA 2 RNA structure
Post by: biohegedus on September 01, 2014, 04:42:08 am

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

Title: Re: DNA 2 RNA structure
Post by: xiangjun on September 01, 2014, 11:17:30 am

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

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University