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Questions and answers => RNA structures (DSSR) => Topic started by: GengshiWu on November 10, 2025, 09:03:36 pm

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Title: Can 3DNA DSSR handle Left-handed DNA?
Post by: GengshiWu 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
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on November 11, 2025, 12:41:46 am
Hi Gengshi,

Thank you for sharing details about your L-DNA structure (mirror image of standard B-DNA). It seems to represent a novel form, and I plan to investigate it further. If feasible, I will update DSSR to accommodate this new form.

Best regards,

Xiang-Jun
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on November 11, 2025, 09:19:56 pm
Hi Gengshi,

I've checked the two PDB files you uploaded: a standard B-DNA model (ending with aligned2Z.pdb), and its mirror-image (L-DNA), with x-coordinates negated (ending with aligned2Z_i_x.pdb). For clarity, I've extracted the first 6 atoms from each file, so readers easily see the differences.

# a standard B-DNA model          x
ATOM      1  P    DA A   1       0.621   9.421  -1.028  1.00  0.00           P
ATOM      2  O1P  DA A   1       0.606  10.783  -1.583  1.00  0.00           O
ATOM      3  O2P  DA A   1       1.439   9.186   0.166  1.00  0.00           O
ATOM      4  O5'  DA A   1      -0.863   8.945  -0.676  1.00  0.00           O
ATOM      5  C5'  DA A   1      -1.693   8.405  -1.689  1.00  0.00           C
ATOM      6  C4'  DA A   1      -2.528   7.255  -1.154  1.00  0.00           C

# a mirror-image, with x-coordinates negated
ATOM      1  P    DA A   1      -0.621   9.421  -1.028  1.00  0.00           P
ATOM      2  O1P  DA A   1      -0.606  10.783  -1.583  1.00  0.00           O
ATOM      3  O2P  DA A   1      -1.439   9.186   0.166  1.00  0.00           O
ATOM      4  O5'  DA A   1       0.863   8.945  -0.676  1.00  0.00           O
ATOM      5  C5'  DA A   1       1.693   8.405  -1.689  1.00  0.00           C
ATOM      6  C4'  DA A   1       2.528   7.255  -1.154  1.00  0.00           C


Mathematically, this is a simple operation, but you have created a hypothetical DNA type that is unknown to DSSR. Nevertheless, DSSR is functioning as intended:

  Note: a helix is defined by base-stacking interactions, regardless of bp
        type and backbone connectivity, and may contain more than one stem.
      helix#number[stems-contained] bps=number-of-base-pairs in the helix
      bp-type: '|' for a canonical WC/wobble pair, '.' otherwise
      helix-form: classification of a dinucleotide step comprising the bp
        above the given designation and the bp that follows it. Types
        include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices,
        '.' for an unclassified step, and 'x' for a step without a
        continuous backbone.
      --------------------------------------------------------------------
  helix#1[1] bps=40
      strand-1 5'-AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG-3'
       bp-type    ||||||||||||||||||||||||||||||||||||||||
      strand-2 3'-TTTTTTTTTTAAAAAAAAAAGGGGGGGGGGCCCCCCCCCC-5'
      helix-form  .......................................


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

Yes, that is correct. DSSR can see this is a left-handed helix, but it (currently) does not recognize your L-DNA form.

Along the line, one could imagine another form where y-coordinates are flipped. What would it be called? How would DSSR suppose to classify it?

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

In principle, yes. One just needs to incorporate the domain-specific knowledge into the DSSR code. I need to know more about your L-DNA before considering how to do that.

Best regards,

Xiang-Jun
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: GengshiWu 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
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on November 15, 2025, 10:31:55 am
Hi Gengshi,

Thanks for your clarification regarding the naming of L-DNA, referring to the L-2-deoxyribose. It is a nice coincidence it is also left-handed.

Your L-DNA actually has prompted me to think more about this new (hypothetical) form of DNA, which is left-handed but with a B-type helix, by simply reversing x-coordinates of the classic B-DNA model. I can now have a clear mental image of this L-DNA: left-handed, with base-pairs flipped along the long axis. These are the two key features of Z-DNA, which characterizes a zig-zag backbone of CG repeats. The L-DNA, however, has a smooth backbone, as in B-DNA.

With this knowledge, it is not hard to classify L-DNA automatically with DSSR. I may consider to add the --L-DNA option specifically for this purpose, not to complicate the default DSSR output. It is after all not a common form, as A-, B-, and Z-form DNA. I would to see more examples of such L-DNA.

It is questions like yours that make DSSR more relevant and useful. I always appreciate users' feedback and encourage them to ask questions, sharing their experiences (both good and bad), freely and openly on the 3DNA Forum. Even in the age of AI, I still believe that there is no replacement for the human touch. I watch the 3DNA Forum closely and am quick to respond to users’ questions and concerns.

Best regards,

Xiang-Jun



Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: GengshiWu on November 18, 2025, 01:30:40 pm
Xiang-Jun,

Thank you for considering an adding the L-DNA option in DSSR. And I think your summary captures exactly what I mean by L-DNA: a left-handed helix with B-like geometry and a smooth backbone, distinct from Z-DNA. At this moment, I don’t have additional L-DNA examples. But I’ll share more on the forum with the community as I'll need to generate and study them.

Best,
Gengshi Wu
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: Di_Liu on November 18, 2025, 04:05:42 pm
Hi Xiang-Jun,

L-DNA is totally synthetic from the mirror-image sugar, but now is very widely used. Here is a brief intro from Glen: https://www.glenresearch.com/reports/gr33-21
Let me further clarify: reversing the x-coordinates is actually performing the reflection about the yz plane, which is a special case. More generally, L-DNA can be generated by performing the reflection about any plane.
Thanks for considering to handle L-DNA with DSSR! L-sugar could be readily determined from the chiral carbon atoms on the sugar.

Di
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: GengshiWu on November 18, 2025, 05:56:47 pm
Thank you for the clarification!
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: Di_Liu on November 18, 2025, 06:24:18 pm
By the way, here is a pdb structure containing both L-DNA and L-RNA: https://www.rcsb.org/structure/4WB3
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on November 18, 2025, 09:25:57 pm
Hi Di and Gengshi,

Thanks for the additional information. They are exactly the kind of information I was looking for.


I'll study them carefully, and try to implement an option in DSSR to handle L-DNA atuomatically. I'll keep you updated.

Best regards,

Xiang-Jun
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on December 08, 2025, 11:36:31 pm
Hi Di and Gengshi,

Thanks for bringing L-DNA to my attention. I've updated DSSR to v2.7.0-2025dec09, which automatically recognizes L-DNA/RNA steps. Using your model PDB (`b40-rb10.5_out_minimized_aligned2Z_i_x.pdb`) as an example, the new DSSR output is as follows:

Code: [Select]
  helix#1[1] bps=40
      strand-1 5'-AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG-3'
       bp-type    ||||||||||||||||||||||||||||||||||||||||
      strand-2 3'-TTTTTTTTTTAAAAAAAAAAGGGGGGGGGGCCCCCCCCCC-5'
      helix-form  LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
I’ve also tested it on PDB entry 4wb2, using biological unit 1 in the file 4wb2.pdb1, and the following output was obtained:

Code: [Select]
  helix#1[3] bps=9
      strand-1 5'-gcgugugug-3'
       bp-type    |||||||||
      strand-2 3'-cgcacgcac-5'
      helix-form  LLxL.xLx

Since L-DNA isn't a common form and DSSR may require further improvements to handle it better, I haven’t updated the documentation or the note in the DSSR output yet. Please let me know if the new DSSR output makes sense to you and share any questions or suggestions. Future updates to this feature would be much faster than this initial implementation.

Best regards,

Xiang-Jun
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on December 24, 2025, 10:58:53 am
As a follow-up to my previous response, DSSR v2.7.1-2025dec22 checks the stereochemistry of sugar. For each L-sugar, the JSON output will contain the key/value: "is_L_sugar": true in the nts object.

For example, running the following DSSR command on PDB entry 4WB2:

Code: [Select]
x3dna-dssr -i=4wb2.pdb --json | jq '.nts[] | {nt_id, is_L_sugar}'
will generate the following JSON output (excerpt):

Code: [Select]
......
{
  "nt_id": "D.0G35",
  "is_L_sugar": true
}
{
  "nt_id": "D.0C36",
  "is_L_sugar": true
}
......

In version v2.7.0-2025dec09, DSSR checks for flipped base pairs relative to the backbone direction. In this aspect, the L-form shares the same topology as Z-DNA, and both are left-handed helices. In version v2.7.1-2025dec22, DSSR takes into account the stereochemistry of the sugar to clearly distinguish between L and Z-form DNAs based on their L- and D-sugar configurations.

In this process, DSSR has been enhanced in multiple areas like classification and rebuilding by incorporating the L-form into a comprehensive framework. I highly value user feedback because it provides new insights that I might otherwise overlook. Once I fully grasp an issue, it often leads to an improved version of DSSR.

Xiang-Jun
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: JiaolongBao on June 15, 2026, 09:58:56 pm
Dear Xiang-Jun,

I am currently using DSSR to help me figure out the base pair, step base pair, helical base pair parameters difference between D and L form B-DNA. I just notice this post is regarding L-form DNA recognition and realize you update DSSR in v2.7.1 to acommondate L-DNA is a sense while I am still using a bit outdated version DSSR v2.6.0-2025jul24 to analyze a native B-DNA duplex and its mirror-image counterpart.

Specifically, I used PDB entry 1BNA as the native structure and generated a mirror-image structure by reflecting the X coordinates(x -> -x). I attached the JSON format output file in this post, but anyway I list the sign inversion conclusion here:
Code: [Select]
Shear      : no sign inversion
Stretch    : no sign inversion
Stagger    : sign inversion
Buckle     : sign inversion
Propeller  : sign inversion
Opening    : no sign inversion
Code: [Select]
Shift  : no sign inversion
Slide  : sign inversion
Rise   : no sign inversion
Tilt   : sign inversion
Roll   : no sign inversion
Twist  : sign inversion
Code: [Select]
x-displacement : no sign inversion
y-displacement : sign inversion
helical rise   : no sign inversion
inclination    : sign inversion
tip            : no sign inversion
helical twist  : sign inversionHere which makes me feel confused is that the sign inversion pattern of the base pair parameters is different from that of the step and helical parameters. I understand that if the inversion pattern of bp parameters apply to step/helical bp parameter, such as Twist and Helical Twist will be "no sign inversion" which is impossible since the most distinct difference between native and mirror-image double helix is right and left handed. I looked into X3DNA and also SCHNAaP paper which has detailed description about how to calculate the parameters which makes believe the sign inversion pattern should be same . Probably DSSR has some certain axis direction inversion when calculate step/helical bp parameters which I overlooked.

I am also wondering the DSSR V2.7.1 or the newest version will give out the same conclusion or there is some certain adaption when encounter L-form when calculating the parameters. I will be very grateful to your help and sorry if I misunderstood something.
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on June 16, 2026, 08:30:02 am
Hi JiaolongBao,

Thank you for your follow-up on this topic. The analysis of L-DNA (with mirror-image sugar-phosphate backbones) is a new DSSR feature, added in response to user requests. DSSR can identify the mirror-image sugar components and classify the corresponding steps as L-DNA with a negative twist angle. Running DSSR on your 1BNA_L.pdb file yields the following results:

Code: [Select]
# x3dna-dssr -i=1BNA_L.pdb --more
  helix#1[1] bps=12
      strand-1 5'-CGCGAATTCGCG-3'
       bp-type    ||||||||||||
      strand-2 3'-GCGCTTAAGCGC-5'
      helix-form  LLLLLLLLLLL
    helical-rise:   3.35(0.44)
    helical-radius: 9.37(0.98)
    helical-axis:    0.088    -0.275    -0.958
       point-one:  -16.795    25.817    26.180
       point-two:  -13.557    15.707    -9.067
   1 A.DC1          B.DG24         C-G WC           19-XIX    cWW  cW-W
        bp1-pars:* [-0.42    -0.27    -0.06    -2.76    14.18    -3.67]
       step-pars:  [0.36     0.15     3.52     -3.40    -6.44    -40.31]
       heli-pars:  [0.55     0.11     3.52     9.26     -4.88    -40.94]
        bp2-pars:* [-0.02    -0.27    -0.25    4.45     10.83    -4.02]
       C1'-based:                rise=3.52                 twist=-38.57
       C1'-based:              h-rise=3.52               h-twist=-39.23
...

Regarding the sign inversion pattern of the base-pair and step/helical parameters, you are the first user to raise this question. In the current implementation, certain base-pair parameters are reversed due to the adjustment of the base reference frame, and the corresponding step/helical parameters follow those adjustments. I will examine the source code details and follow up on this topic soon.

From a user perspective, what behavior do you consider most logical? As the DSSR developer, I want the tool to meet user expectations while remaining mathematically consistent. The current implementation satisfies the requirements of Di and Gengshi, who initially requested this feature.

Best regards,

Xiang-Jun
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: JiaolongBao on June 17, 2026, 02:36:37 am
Hi Xiang-Jun,

Thanks for your reply and continued effort looking in to source code of DSSR.

I appreciate that you provide the newest version DSSR output regarding 1BNA_L.pdb. In this case, the sign inversion pattern of base-pair parameter is the same as v2.6.0. However, the sign inversion pattern of step/helical bp parameters looks different with v2.6.0 in terms of shift, slide, tilt, roll, x-disp, y-disp, inclination and tip. Out of curiosity, I also downloaded SCHNAaP and X3DNA source code and use them to analyze the 1BNA_L.pdb, which gives me a more "reasonable" sign inversion pattern. I summarized the sign-inversion patterns in the three attached tables. Here, “Yes” means that the sign of the corresponding parameter is reversed between 1BNA.pdb and 1BNA_L.pdb, while “No” means that the sign is preserved. along with SCHNAaP, X3DNA v2.4, DSSR v2.6 and v2.9 for your reference.

As you can see in the tables, SCHNAaP and X3DNA share the same sign inversion pattern for base-pair and step/helical parameters which looks more intuitive to me. Interestingly, DSSR v2.9 now gives the same sign-inversion pattern as SCHNAaP and X3DNA for the step parameters and helical base-pair parameters. However, for the base-pair parameters, DSSR v2.9 still follows the same pattern as DSSR v2.6, which differs from SCHNAaP and X3DNA for shear, stagger, buckle, and opening.

Based on my understanding of SCHNAaP paper (which has very detailed explanation on how to calculate those parameters, although it is outdated since DSSR is using base reference frame), the calculation of base-pair and step/helical parameters is very similar and I believe mirror-image transformation will lead to same sign inversion pattern. I feel the sign inversion of parameters heavily depends on the axis direction and also which axis is determined by right-handed rule. Anyway, I'm more interested in DSSR how to handle this scenario.

Besides, I also notice when DSSR judge the "sugar-class" of L-sugar may have some issues. I guess DSSR is based on the phase angle to determine the sugar class of sugar which is totally fine to D-sugar while it may not be suitable for L-sugar. I believe the chirality inversion of sugar will not affect the sugar class but phase angle should be definetely inversed. For example, DSSR determine the sugar class of nucleotides in 1BNA_L.pdb is C3'-endo while it should be C2'-endo no matter in D or L form B-DNA.
Code: [Select]
Summary of structural features of 24 nucleotides
  Note: the first five columns are: (1) serial number, (2) one-letter
    shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base
    ring atoms fitted against those in a standard base reference
    frame. The sixth (last) column contains a comma-separated list of
    features whose meanings are mostly self-explanatory, except for:
      turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees
      break: no backbone linkage between O3'(i-1) and P(i)
   1  C ( A.DC1    0.020  anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end
   2  G ( A.DG2    0.025  anti,~C3'-endo,canonical,non-pair-contact,helix,stem
   3  C ( A.DC3    0.024  anti,canonical,non-pair-contact,helix,stem
   4  G ( A.DG4    0.023  anti,~C3'-endo,canonical,non-pair-contact,helix,stem
   5  A ( A.DA5    0.016  anti,~C3'-endo,canonical,non-pair-contact,helix,stem
   ................

I hope our discussion can make DSSR more capable for analysis of L-DNA/RNA. Thanks!

Best regards,
Jiaolong





Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: xiangjun on June 17, 2026, 06:50:45 am
Hi Jiaolong,

Thanks for the detailed explanation—this kind of feedback is exactly what I have been looking for.

I will certainly investigate the sign convention further. In this post, I would like to address the sugar-class issue. Currently, the L-sugar class is determined based on the pseudorotation phase angle, using the exact same criteria as for D-sugars. I have attached the dssr-torsions.txt output for 1BNA_L.pdb. Honestly, I had not paid close attention to this specific aspect of L-DNA before. Please let me know the correct way to determine the sugar class in these cases.

For this type of discussion, a phone call or a video meeting might be more convenient. Please let me know if you would like to connect online or over the line to discuss this topic further.

Best regards,

Xiang-Jun
Title: Re: Can 3DNA DSSR handle Left-handed DNA?
Post by: JiaolongBao on June 17, 2026, 09:08:34 pm
Hi Xiang-Jun,

Certainly! I will email you for a video meeting.

Many Thanks,
Jiaolong

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