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Messages - manish

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Hi Xiang-Jun,

First of all, thanks a lot for your earnest response. With regards to your first query, I am not sure if there are any available software tools for sugar mutations. However, please let me know if you find/are aware of any such tools for sugar mutations. It would be of great help to me.

' Cannot you do it manually? '- I can do it manually but i will have to worry about the dihedral angles and bond length in the case of the mutated sugars and it might be inconsistent with the conformation that i have taken from the fiber model from web x3dna 2.0. So, O2'-C2'-C3'-C4' dihedral is the main cause of my concern.

' How do you consider the sugar conformations (C3'-endo vs C2'-endo) after adding O2' ?'- Ideally, I would like to have the sugar conformations unchanged for the modified bases after addition of O2', if there are no steric clashes. Then, I want to see what changes come up over time to these forcibly retained bases, through MD simulations.

' Do you have a concrete example of such mutations? '- Yes, there are many examples of such mutations in literature. Please go through either of these links to have a rough idea of what I am trying to study:

I would be glad to listen to any of the ideas you have to make these modified sugars. Thanks again for your time and cooperation.


Hi Xiangjun,

My question is related to mutate_bases option in the x3DNA webpage. When I select any pdb file for mutation, it gives me the option of mutating bases like A, T, G, C or U at any position in the selected pdb file. Is it possible to include rNMP apart form dNMP in these mutate_bases option even if my control sequence is composed of dNMP units only?  So basically, i want to keep the base part unchanged but the sugar can be changed from deoxyribose to ribose (Eg- dA to rA or dG to rG as such) with the predefined fiber models.

Thanks a lot for your time


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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.