61
RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last post by GengshiWu on November 18, 2025, 05:56:47 pm »Thank you for the clarification!
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62
RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last 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
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
63
RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last 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
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
64
RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last 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
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
65
RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last 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
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
66
RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last 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.
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:
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?
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
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:
- For the standard B-DNA model, DSSR classifies the dinucleotide step as 'B' correctly.
- For the L-DNA, DSSR cannot classify the dinucleotide steps. and designates them as '.' (see the section below). Also as noted in the header section, DSSR only recognizes the common A-, B-, and Z-form helices.
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
67
RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last 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
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
68
RNA structures (DSSR) / Can 3DNA DSSR handle Left-handed DNA?
« Last 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
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
69
MD simulations / Re: generate DNA pdb file for Gromacs
« Last post by rkumar on September 29, 2025, 07:45:22 am »Hi,
Another option could be the Nucleic Acid Builder (NAB) (available in AmberTools) to model the 3D structure of DNA for MD simulations (https://ambermd.org/tutorials/basic/tutorial1/section2.php). I have used this one to model the DNA and performed the MD simulations.
Thanks,
Rajendra
Another option could be the Nucleic Acid Builder (NAB) (available in AmberTools) to model the 3D structure of DNA for MD simulations (https://ambermd.org/tutorials/basic/tutorial1/section2.php). I have used this one to model the DNA and performed the MD simulations.
Thanks,
Rajendra
70
MD simulations / Re: generate DNA pdb file for Gromacs
« Last post by xiangjun on September 13, 2025, 11:13:30 am »Hi Mengyao,
Thanks for posting your question on the 3DNA Forum.
I am not familiar with TNA. From your description, TNA is a non-natural nucleic acid structure with a tetrose, instead of pentose, sugar. Given further information about TNA, I may be able to help build a model as a starting structure for MD simulations.
Best regards,
Xiang-Jun
Thanks for posting your question on the 3DNA Forum.
Quote
We are currently attempting to model non-natural nucleic acid structures. We would like to know if it is possible to predict the structure of threose nucleic acid (TNA). Is this feature already included in some of the tools ?
The main difference between TNA and DNA or RNA lies in the ribose. It is known that DNA (RNA) contains a pentose sugar, while TNA contains a tetrose sugar. Therefore, the connection sites of the phosphodiester bonds are different.
I am not familiar with TNA. From your description, TNA is a non-natural nucleic acid structure with a tetrose, instead of pentose, sugar. Given further information about TNA, I may be able to help build a model as a starting structure for MD simulations.
Best regards,
Xiang-Jun
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