Print Page - Contour of dsDNA/dsRNA

Questions and answers => RNA structures (DSSR) => Topic started by: tengxj12345 on April 30, 2025, 09:48:25 pm

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.3 (DSSR Manual) · Homepage

Title: Contour of dsDNA/dsRNA
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

Title: Re: Contour of dsDNA/dsRNA
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

Title: Re: Contour of dsDNA/dsRNA
Post by: tengxj12345 on April 30, 2025, 10:44:44 pm

Sure. I attached my pdb file. I uploaded to the webserver and generated summary.txt.

The last section of the file (Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step) was then used to draw the centroids. I can get the same results bu running it on my local computer (find_pair and analyze).

Title: Re: Contour of dsDNA/dsRNA
Post by: xiangjun on April 30, 2025, 11:38:47 pm

Thanks for your clarification. The two attachments are very helpful. Now I can use the following 3DNA commands to reproduce the results:

Code: Bash

find_pair coor_7972.pdb | analyze

The output file "coor_7972.out" has exactly the same parameter as the attached file "summary.txt".

Now back to your question:

Quote

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?

The "strange" behavior you are observing is due to the sensitivity of helical parameters to local structural variations. There is nothing wrong as far as 3DNA goes. To verify this, you could try the following two things:

* Build a perfectly regular fiber RNA duplex model using the command below, and repeat your procedure. You should see a straight helix as expected. For example, see Figures 1 and 9 of the 2003 3DNA paper (https://academic.oup.com/nar/article/31/17/5108/1192167).

Code: Bash

fiber -seq=AAAAAAAAAA -rna fiber-RNA-A10.pdb
# or better yet, using DSSR v2.5.2
x3dna-dssr fiber --rna-duplex --seq=A10 -o=dssr-fiber-RNA-A10.pdb

* With the parameters from 3DNA analyze output (bp_step.par or bp_helical.par), you can run rebuild to generate a structure. The RMSD between the original structure and the rebuilt one should be close to 0 for base + C1' atoms. If you analyze the rebuilt structure, you should get virtually identical helical parameters as for the original structure. The analyze/rebuild reversibility is one of the core features of 3DNA and DSSR, originating from the SCHNAaP/SCHNArP pair of programs based the CEHS algorithm.

Hope this helps! Basically, what you are observing is the expected behavior of 3DNA.

That being said, for visualization purposes, one might want to smooth the local variations using Bezier curves or similar methods.

Best regards,

Xiang-Jun

Title: Re: Contour of dsDNA/dsRNA
Post by: tengxj12345 on May 01, 2025, 12:28:19 pm

Thanks for your detailed explanation. I will check it out.

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