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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:
1- https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201600385
2- https://pubs.acs.org/doi/10.1021/bi201710q

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.

 

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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

Manish

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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.