Recent Posts

21

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

22

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

23

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.

# 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  .......................................

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?

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

24

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

25

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

26

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

27

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.

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

28

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by xiangjun on September 13, 2025, 11:04:50 am »

The DNA pdb file generated by X3DNA has only A T C G, but no terminal base, e.g. A3, A5, T3, T5, ...
How to use X3DNA generate a pdb file with terminal bases?

DSSR has superseded X3DNA, and it can be used to generate a PDB file with terminal bases as you requested. See the following example:

Code: [Select]

# Generate a regular B-DNA model with sequence (AAAAAATTTTTT; shortened as A6T6)
x3dna-dssr fiber --b-dna --seq=A6T6 -o=A6T6-BDNA.pdb

# Mutate residue name 5'-A on chains A and B from the detault 'A' to 'A5':
x3dna-dssr mutate --entry='num=1 to=A5' -i=A6T6-BDNA.pdb -o=A5-both.pdb
A portion of the output PDB file A5-both.pdb is shown below:

REMARK PDB mutated using DSSR
REMARK DSSR mutate: A.A1 to A5
ATOM      1  P    A5 A   1      -0.356   9.218   1.848  1.00  0.00           P
ATOM      2  OP1  A5 A   1      -0.311  10.489   2.605  1.00  0.00           O
ATOM      3  OP2  A5 A   1      -1.334   9.156   0.740  1.00  0.00           O
ATOM      4  O5'  A5 A   1       1.105   8.869   1.295  1.00  0.00           O
ATOM      5  C5'  A5 A   1       2.021   8.156   2.146  1.00  0.00           C
ATOM      6  C4'  A5 A   1       2.726   7.072   1.355  1.00  0.00           C
ATOM      7  O4'  A5 A   1       1.986   5.817   1.352  1.00  0.00           O
ATOM      8  C3'  A5 A   1       2.952   7.370  -0.127  1.00  0.00           C
ATOM      9  O3'  A5 A   1       4.210   6.832  -0.518  1.00  0.00           O
ATOM     10  C2'  A5 A   1       1.848   6.598  -0.850  1.00  0.00           C
ATOM     11  C1'  A5 A   1       1.913   5.344   0.016  1.00  0.00           C
ATOM     12  N9   A5 A   1       0.717   4.478  -0.101  1.00  0.00           N
ATOM     13  C8   A5 A   1      -0.592   4.850  -0.293  1.00  0.00           C
ATOM     14  N7   A5 A   1      -1.424   3.839  -0.355  1.00  0.00           N
ATOM     15  C5   A5 A   1      -0.609   2.726  -0.193  1.00  0.00           C
ATOM     16  C6   A5 A   1      -0.886   1.349  -0.163  1.00  0.00           C
ATOM     17  N6   A5 A   1      -2.111   0.835  -0.301  1.00  0.00           N
ATOM     18  N1   A5 A   1       0.154   0.505   0.016  1.00  0.00           N
ATOM     19  C2   A5 A   1       1.380   1.020   0.154  1.00  0.00           C
ATOM     20  N3   A5 A   1       1.767   2.294   0.144  1.00  0.00           N
ATOM     21  C4   A5 A   1       0.712   3.105  -0.035  1.00  0.00           C
ATOM     22  P     A A   2       5.130   7.667  -1.527  1.00  0.00           P
ATOM     23  OP1   A A   2       5.914   8.669  -0.770  1.00  0.00           O
ATOM     24  OP2   A A   2       4.303   8.192  -2.635  1.00  0.00           O

In addition to the above question, is it possible to generate a pdb file that is fully compatible with Gromacs. Now there are some incompatible things. Such as Gromacs using DA, DT, DC, DG, rather than A, T, C, G.

I'm not sure the exact requirements for compatibility with Gromacs, but you can easily mutate 'A' to 'DA' etc using DSSR mutate subcommand as shown below:

Code: [Select]

x3dna-dssr mutate --entry='A:DA;T:DT' -i=A6T6-BDNA.pdb -o=DA-DT.pdb
See the DSSR User manual for more details.

29

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by xiangjun on September 13, 2025, 10:45:00 am »

Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.

With DSSR (here v2.6.0-2025jul24 is used), you can use the following command to generate a PDB file for your (DNA) sequence:

Code: Bash

1. x3dna-dssr fiber --seq= A6C10 --repeat =2 --model =RNA
2. x3dna-dssr fiber --rna -o=rna -ss.pdb
3. x3dna-dssr fiber --rna -ds -o=rna - duplex .pdb # --rna -double , --RNA - duplex
4. x3dna-dssr fiber --g4 -o=g4.pdb
5.  
6. # The following four commands lead to the same results
7. x3dna-dssr fiber --seq= A6TC9 --repeat =2 -o=B1.pdb
8. x3dna-dssr fiber --B-DNA --seq= A6TC9 --repeat =2 -o=B2.pdb
9. x3dna-dssr fiber --model =b-dna --seq= A6TC9 --repeat =2 -o=B3.pdb
10. x3dna-dssr fiber --model =b-dna --seq=A6 -T-C9 --repeat =2 -o=B4.pdb
11.  
12. x3dna-dssr fiber --seq= A1000 --mmcif - output # B-DNA , in mmCIF output format
13.  
14. x3dna-dssr fiber --pauling --seq=A6 # three strands , all A6
15. x3dna-dssr fiber --pauling --seq=C6: # one strand : C6 ( A )
16. x3dna-dssr fiber --pauling --seq=A6:G2 # two strands : A6 ( A ) and G2 ( B )
17. x3dna-dssr fiber --pauling --seq=A6 :: G2 # two strands : A6 ( A ) and G2 ( C )
18. x3dna-dssr fiber --pauling --seq =: U3:G2 # two strands : U3 ( B ) and G2 ( C )
19. x3dna-dssr fiber --pauling -dna --seq=U8 --repeat =4 # U converted to T

See the DSSR User Manual, especially Section "5.2 Regular helical models (fiber)" for more details.

30

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by ZMY on August 28, 2025, 07:05:11 am »

Dear all,

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.

Thank you in advance,
Best regards, Mengyao