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RNA structures (DSSR) / Re: Rebuilding circular Z-DNA
« Last post by xiangjun on April 24, 2025, 11:07:20 pm »Hi @Di_Liu,
Nice progress! Using DSSR, I can see clearly the 84 isolated G-C pairs along the circular structure. I will consider adding an option to "x3dna-dssr tasks" subcommand to replace these G-C pairs with GpC dinucleotide steps. Before doing that, it helps to manually replace a few of these G-C pairs with GpC steps to see how the structure looks like. These examples would also server as test cases to validate the new option.
Yes, it does make sense. Please go ahead and post the details of your construction process. It may take several iterations to get the desired results. The more concrete our discussions are, the better we can understand each other.
Best regards,
Xiang-Jun
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I tried to make some progress on constructing a 168-bp circular Z-DNA structure. What I have achieved so far is determining the positions of the repeating units (each being a CG dimer) along the ring. Each position currently serves as a placeholder (a G:C pair; 84 in total), to be replaced by a Z-DNA dimer unit.
I'm attaching a screenshot of the current structure, as well as the corresponding PDB file. I think Xiang-Jun might be able to work his "tasks" magic to align and insert the Z-DNA dimer units into the specified positions.
Nice progress! Using DSSR, I can see clearly the 84 isolated G-C pairs along the circular structure. I will consider adding an option to "x3dna-dssr tasks" subcommand to replace these G-C pairs with GpC dinucleotide steps. Before doing that, it helps to manually replace a few of these G-C pairs with GpC steps to see how the structure looks like. These examples would also server as test cases to validate the new option.
Quote
If you think this direction makes sense, I’d be happy to post the detailed process of how I constructed this circle.
Yes, it does make sense. Please go ahead and post the details of your construction process. It may take several iterations to get the desired results. The more concrete our discussions are, the better we can understand each other.
Best regards,
Xiang-Jun