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Dear all,
I am working on the structural modeling of non-canonical G-quadruplexes (G4). Specifically, I am trying to build a monomolecular G4 model characterized by inversions of polarity (alternating 5'-3', 3'-3', 3'-5', and 5'-5' linkages) within the G-tracts.
I am looking for some guidance on how to build the starting structure: While DSSR is excellent at analyzing and rebuilding standard G4 topologies, i am not sure if it can handle these specific phosphodiester bond inversions.
Does DSSR have a built-in way to recognize and validate a chain that contains 3'-3' or 5'-5' linkages, or will it treat them as broken chains during analysis?
Are there specific commands in the latest DSSR releases (or via the mutate module) that allow for inverting the direction of a specific block of residues while maintaining the G-tetrad stacking geometry?
I am looking for a general methodology for handling these "inverted" backbone topologies in a way that remains compatible with subsequent Molecular Dynamics setups.
Once I find a stable workflow, I will be happy to summarize the steps for the community as per the forum guidelines.
Any suggestion is welcome!
Thank you for your time and for this useful resource.
Best
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Hi muha,
Thanks for posting on the Forum, and sorry for the late reply.
I understand your aim to build a unimolecular G-quadruplex model with alternating 5'-3', 3'-3', 3'-5', and 5'-5' linkages. DSSR does not have a built-in option for building such models, and I am not aware of any other software that can do this. In my understanding, this would require a combination of DSSR and a 3D manual editing tool to adjust the polarity of the linkages.
As far as analysis is concerned, DSSR should be able to identify G-tetrads, and may take each tract as broken chains. We need specific examples to show how DSSR should behave in these cases. I will consider modifying DSSR to handle these cases if feasible.
Best regards,
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