Messages

1

RNA structures (DSSR) / Building G-quadruplexes

« 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.

2

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

« on: April 23, 2025, 02:39:29 am »

My work focuses on molecular dynamics simulations of Z-DNA and its interactions with binding proteins. I'm particularly interested in understanding the mechanisms that stabilize Z-DNA, which is inherently less stable than B-DNA.
To explore this, I used the crystal structure of the ADAR1 protein bound to a short Z-DNA segment. Since the original segment was quite short, I wanted to extend the Z-DNA backbone. With your help, I was able to successfully simulate this extended structure. However, I encountered challenges in reproducing the specific protein–Z-DNA interactions observed in the crystal structure during my simulations. I believe this is due to multiple non-specific interactions forming between the DNA and the protein, which may mask or override the specific contacts I'm trying to study. It is not a Z-DNA remodeling problem but I am working on understanding Z-DNA stability.

In addition to Z-DNA, I also work on other non-canonical DNA structures, particularly G-quadruplexes (G4s). I’m developing a method to construct ideal G-quadruplex models from sequence data by first arranging guanine bases into tetrads, then building in the backbone and loop regions. As @Di_Liu suggested, I believe a similar model-building strategy could be applied to Z-DNA, to help generate consistent and realistic structures. What do you think about this approach or direction?

Thank you!

3

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: April 23, 2025, 01:55:34 am »

I apologize once again. I look forward to the blogpost and will check out the thread "Rebuilding circular Z-DNA". I would be happy to contribute in any way I can.

4

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: April 21, 2025, 11:22:48 pm »

Apologies for it took a while to reply. Thank you for your help with the structure! I used phenix to minimise like you suggested and I can use it for my analysis now. I would also look forward to Z-DNA backbones being included in DSSR modeling functionalities.

5

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 17, 2025, 09:21:03 am »

Sorry! I could download it now. It was probably an issue with my browser.

6

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 17, 2025, 08:17:00 am »

Thank you so much! But I am unable to properly download the pdb file. I will try to follow the method you mentioned about in your previous reply.

7

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 14, 2025, 06:05:18 am »

Thank you for your quick responses!
My input structure is the PDB structure 1QBJ. It is a 6nt DNA. I have attached a picture. Without using the x3dna_utils, even without extending, the backbone cannot  be modelled due to the distance of O3' and P being over 4.5 and throws the following error. However, I also tested with the fiber model of Z-DNA to understand how it works with Z-DNA. I found that besides the backbone not being modelled which is because of the PDB dataset not being since I'm not using x3dna_utils, rebuild could model the bases as separate molecules. So, this is possibly the issue with my Z-DNA crystal structure model.

Another observation was, previously, for the crystal structure of BDNA complexed with the protein, I tried to manually extend the DNA in pymol but due to the terminal base positions, I could not properly build the double helix. But after analyze and rebuild, I could. So I assume it is due to standardization of the structure after rebuild. However, there is a problem with this method for Z-DNA. Even if I manage to standardize the structure, pymol does not offer building Z-DNA. So, I was wondering if I could add the extended DNA before rebuild. As you suggested, I modified the bp_step.par file since that is the file used as input for rebuild. Is that the correct way? I apologize if I am asking too many questions.   

8

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 13, 2025, 02:23:03 pm »

I have a PDB structure of Z-DNA-protein complex that I wanted to simulate. Before simulation, I wanted to make the DNA longer to avoid the issue of the protein interacting with any of the terminal bases. I can use the following commands to achieve this in case of B-DNA:

find_pair 1MNN.pdb 1mnn.bps
x3dna_utils cp_std bdna
rebuild -atomic bp_step.par extended_dna.pdb

But x3dna_utils does not take zdna as an argument so I was wondering how I can do it?

9

General discussions (Q&As) / Rebuilding Z-DNA

« on: March 13, 2025, 02:10:17 pm »

I was wondering if there is a way to rebuild Z-DNA with rebuild module in the local installation of x3DNA. I know it works for B-DNA and A-DNA and I can make a Z-DNA fiber model as well but I couldn't find a direct way to extend an existing Z-DNA structure. Is there a workaround which I can try? Thank you in advance.