Recent Posts

51

RNA structures (DSSR) / Re: Contour of dsDNA/dsRNA

« Last post by xiangjun on April 30, 2025, 10:31:11 pm »

Hi Xiaojing,

Thanks for posting on the 3DNA Forum. Could you please provide details about how you generated the contour plot for dsDNA/dsRNA you attached? These would include the PDB or mmCIF coordinates file, and the exact DSSR/3DNA commands you used. The goal is reproducibility and to help others understand the process better.

Best regards,

Xiang-Jun

52

RNA structures (DSSR) / Contour of dsDNA/dsRNA

« Last post by tengxj12345 on April 30, 2025, 09:48:25 pm »

Hello,

I tried to get the contour of dsDNA/dsRNA structures. I think the output from helical section should be it. When I plot the positions of local helical axis along with my pdb, it seems quite strange. The helix doesn't follow the structure of my DNA well. Is there anything wrong, or there are other output can better represent the contour?

Thanks,
Xiaojing Teng

53

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by xiangjun on April 30, 2025, 08:40:24 am »

Hi Di,

How about the attached results? Does it meet your expectations?

Best regards,

Xiang-Jun

54

RNA structures (DSSR) / Re: Building G-quadruplexes

« Last post by xiangjun on April 29, 2025, 02:01:05 pm »

Hi shr,

I've split your response from the thread "Rebuilding circular Z-DNA" into its own thread for better organization and discussion.

It a nice start with the first G-tetrad. Please add more features to your GQ-gen.py script so it can at least build a complete G-quadruplex structure. I'll chime in with some suggestions to your project, while I'm working on adding proper Z-DNA backbone to DSSR-enabled models.

Best regards,

Xiang-Jun

55

RNA structures (DSSR) / Building G-quadruplexes

« Last post by shr on April 29, 2025, 12:03:42 pm »

I am writing this code for GQ structure generation from sequence which can be found here https://github.com/sHr3y4s1/GQ-gen. I have just written this for the first G-track but this can be iterated to create more and then building in loops. I have attached an image of the output of this code. I don't know if this is the best way to do it but I am trying to create a basic canonical structure with specific topologies which can be energy minimized with an ion. I was thinking of a similar way for creating circular Z-DNA structures as well.

56

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by xiangjun on April 25, 2025, 02:34:26 pm »

Hi Di,

Thanks for providing further details on how the structure was generated. Such contextual information is always helpful and serves as a valuable reference for the automated approach we aim to develop.

I will take a closer look at the topic and hopefully could come up something to share by next week. Ad hoc solution is easier to implement but I am keen for a systematic approach as mentioned briefly in my previous response.

Best regards,

Xiang-Jun

57

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by Di_Liu on April 25, 2025, 01:37:09 pm »

Hi Xiang-Jun, I used UCSF Chimera to manually align the dimer units onto G-C pair. It's very difficult to describe it in words and make it reproducible, and that's why I think it would be fantastic if you can help with it by slightly adjusting the codes you already have for generating atoms from helical parameters. 

58

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by xiangjun on April 25, 2025, 07:40:54 am »

Hi Di,

This looks good. Please provide the commands used to generate the structures, for example, as I did in the blogpost on "Building extended Z-DNA structures with backbones using DSSR". Every detail counts for reproducibility.

Moreover, I would also consider the case where C-G pairs instead of G-C pairs are present in the structure. Or all 168 pairs with CGCG... sequence. I've thought about the case, and I think what we are trying to acheive fit under the general category of mutated backbones, given the atomic coordinates of base atoms. This is in contrast to the mutating bases feature currently implemented in `mutate_bases` in 3DNA and the `x3dna-dssr mutate` subcommand in DSSR.

Best regards,

Xiang-Jun

59

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by Di_Liu on April 25, 2025, 02:12:11 am »

Hi Xiang-Jun,

I manually aligned 5 dimer units onto the circle. As expected, it works. Only very minor adjustment of bond angles and lengths are required later. I'm attaching the screenshot and the pdb file.

Di

60

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by xiangjun on April 24, 2025, 11:07:20 pm »

Hi @Di_Liu,

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.

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