Messages

1

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 14, 2025, 05:37:28 pm »

Dear Xiang-Jun,

One thing to clarify: My previous naming of L-DNA and B-DNA was confusing. Although L-DNA forms a left-handed B-type helix, the “L” in L-DNA refers to the sugar chirality (L-2-deoxyribose), not helix handedness. By contrast, the DSSR fiber B-DNA uses D-2-deoxyribose. So, it is also called D-DNA.

With this being said, L-DNA is just the enantiomer (non-superimposable mirror image) of D-DNA. The mirror reflection changed the three chiral carbons of deoxyribose (C1′, C3′, C4′) from R–S–R (D-DNA) to S–R–S  (L-DNA).

Thank you for your time and dedication to DSSR!
Best,
Gengshi Wu

2

RNA structures (DSSR) / Can 3DNA DSSR handle Left-handed DNA?

« on: November 10, 2025, 09:03:36 pm »

Dear Xiang-Jun,

Our lab is currently studying left-handed DNA (L-DNA). I’d like to clarify that by L-DNA we mean the mirror image of standard B-DNA, rather than the L-DNA fiber model included in the 3DNA DSSR library.

Specifically, our structure (b40-rb10.5_out_minimized_aligned2Z_i_x.pdb) was generated by applying a mirror transformation to a standard B-DNA model (b40-rb10.5_out_minimized_aligned2Z.pdb) that we constructed using the DSSR fiber B-DNA model but with modified parameters for 10.5 bp/turn.

When we analyzed this mirror-image L-DNA with x3dna-dssr analyze, the program successfully identified the helix start and end points (as shown in the attached image), but the helix form was not recognized as L-DNA.

My questions are:

1. Is my understanding correct that DSSR can identify the geometry but does not recognize the form of our L-DNA?

2. Is there any way to make DSSR recognize the form of our L-DNA?

Thank you for your time and and for updating this excellent tool!
I also attached the two files mentioned above

Gengshi Wu

3

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« on: August 03, 2025, 07:37:32 pm »

Hi Xiang-Jun,

Thank you for your response!

4

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« on: August 01, 2025, 08:41:06 pm »

Hi Xiangjun,

Thank you for your explanation of the tilt in the rebuilt model,

To clarify our question, we extract parameters and rebuild because the B-DNA model generated with -fiber has 10 bp/turn, but we want a 10.5 bp/turn helix. To make it 10.5 bp/turn, we modify all twist values (except the last row) in dssr-B-DNA-A36-step.txt to 34.2857 (360°/10.5) before rebuilding.

Our goal is for the 10.5 bp/turn helix to align perfectly with the Z-axis, like the original fiber model. But as you noted, rebuilding positions the structure relative to its first base pair, causing some tilt.

Is there a way to directly generate a -fiber DNA helix with 10.5 bp/turn aligned to the Z-axis, avoiding parameter extraction and rebuilding?

5

RNA structures (DSSR) / Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« on: July 31, 2025, 10:46:10 pm »

Hi Xiang-Jun, I have been working with the 3DNA DSSR tools to generate a B-DNA helix and encountered an unexpected issue with the axis alignment after reconstruction. Here are the steps that I performed:

1. Generated a 36 bp B-DNA helix using: x3dna-dssr fiber --model=B-DNA --seq=A36 -o=dssr-B-DNA-A36.pdb
    -When I open the dssr-B-DNA-A36.pdb file that I generated in UCSF Chimera, the helix axis aligns perfectly with the 3D coordinate z-axis.

2. Extracted parameters using: x3dna-dssr analyze --rebuild -i=dssr-B-DNA-A36.pdb -o=dssr-B-DNA-A36-expt.out
    -Then, I renamed the extracted step and helical parameter files for clarity: mv dssr-dsStepPars.txt dssr-B-DNA-A36-step.txt  mv dssr-dsHeliPars.txt dssr-B-DNA-A36-heli.txt

3. Reconstructed the structure using the step parameter file with: x3dna-dssr rebuild --backbone=B-DNA --par-file=dssr-B-DNA-A36-step.txt -o=dssr-B-DNA-A36-rb10.5.pdb
    - However, when I open the reconstructed pdb file in Chimera, the helix axis is slightly tilted relative to the z-axis.

Could you please advise whether this tilt is expected due to reconstruction? Or is there a recommended way to maintain the original axis alignment during rebuilding?

Thanks!