Rebuilding circular Z-DNA

[Di_Liu]

Hi Xiang-Jun, I think three steps are needed for creating such a Z-DNA ring or more generally, any Z-form helical structures:

(1) Obtaining a helical parameter file in a similar way as the A- or B-form helices;
(2) Creating the atoms of the bases based on the helical parameter file;
(3) Putting the other atoms of the sugar and phosphate groups based on the position of the bases' atoms (there are only two conformations corresponding to the pyrimidines and purines, respectively).

Do you prefer that I start a new thread on this topic?

Thanks!

[xiangjun]

Hi Di,

Thanks for chiming in on the topic on modeling Z-DNA structures with proper backbones. User @shr "would also look forward to Z-DNA backbones being included in DSSR modeling functionalities."

Let's continue the discussion through this thread. Your special interest in circular Z-DNA structures will also be taken into account.

In addition to splitting the topic as a new thread, I have also moved the thread under the Section on RNA structures (DSSR) from "General discussions (Q&As)". I aim to develop this feature within DSSR. As noted previously, the classic 3DNA suite of programs has been superseded by DSSR.

If you and @shr could share what you have done so far, I would very much like to see. The more concrete examples, the better.

Best regards,

Xiang-Jun

[shr]

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!

[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.

If you think this direction makes sense, I’d be happy to post the detailed process of how I constructed this circle.