How to view triplex DNA with designed sequence via X3DNA?

[Coldcrow]

Dear Dr. Xiang-Jun Lu：
      I need to visualize triplex DNA via 3DNA. Firstly, the DNA sequence is designed by myself, which is AAGGAAGAAG TTTA CTTCTTCCTT CTTG TTCCTTCTTC. I need your help to transform the sequences into PDB format. It is worth noting that the sequence is special for its self-complementary TAT and CGC triple base pair. And then, could you show me how to operate command line to generate PDB format using my own sequence?
      Recently, I have read similar method in one paper. In the Molecular Dynamis Simulations part of EXPERIMENTAL SECTION, the author used X3DNA program to generate PDB file. However, in your published paper in Nature protocol(2008), you mentioned that 3DNA had to process PDB file. I do not think this method in this paper was advisable. What do you think? This paper is enclosed in the attachment.

[xiangjun]

Molecular Dynamics Simulations. The fiber module of the X3DNA program⁴⁰ has been used to generate the PDB file template of the triple-helix model, exclusively formed by TAT sequence repetitions. The nucleotide sequence of the strands composing the triple helix has been modified through the X3DNA mutate_bases module⁴⁰ in order to match the designed oligonucleotides sequences. ...

The above citation represents an expected use-case of the modeling features of the 3DNA suite of programs. Note that 3DNA is a software tool for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures. The description is clear, and should be simple to follow.

I need to visualize triplex DNA via 3DNA.

It is not clear to me what you mean here.

Firstly, the DNA sequence is designed by myself, which is AAGGAAGAAG TTTA CTTCTTCCTT CTTG TTCCTTCTTC. I need your help to transform the sequences into PDB format. It is worth noting that the sequence is special for its self-complementary TAT and CGC triple base pair.

You are talking about a triplex DNA, which should have three strands. From the above description, I am not sure how the sequence is divided into three segments for the triplex. Please clarify.

And then, could you show me how to operate command line to generate PDB format using my own sequence?

The answer should become clear once the above steps are followed.

Best regards,

Xiang-Jun

[Coldcrow]

1-I need to visualize triplex DNA via 3DNA.
   Explanation:3DNA is a software tool for the visualization of 3-dimensional nucleic acid structures. My designed DNA sequence (5'-AAGGAAGAAG TTTA CTTCTTCCTT CTTG TTCCTTCTTC-3') was single strand and could form triple helix via Waston-Crick hydrogen bond and Hoogsteen hydrogen bond. The base pair is shown as follow. In the Figure, the round dots represent Waston-Crick hydrogen and the square dots represents the Hoogsteen hydrogen bond.

2- About PDB format file.
   In your published paper in Nature protocol(2008), you mentioned that 3DNA had to process PDB file. So How to transform my designed sequence(5'-AAGGAAGAAG TTTA CTTCTTCCTT CTTG TTCCTTCTTC-3') into PDB file to process 3DNA software.

3-About command line.
   After obtaining the PDB file containing my designed sequence, could you show me the code of  command line to visualize the 3-dimensional triplex helix structure?

   

[xiangjun]

Thanks for the follow-up, which makes your point clearer. Let's proceed step-by-step.

1-I need to visualize triplex DNA via 3DNA.
   Explanation:3DNA is a software tool for the visualization of 3-dimensional nucleic acid structures. My designed DNA sequence (5'-AAGGAAGAAG TTTA CTTCTTCCTT CTTG TTCCTTCTTC-3') was single strand and could form triple helix via Waston-Crick hydrogen bond and Hoogsteen hydrogen bond. The base pair is shown as follow. In the Figure, the round dots represent Waston-Crick hydrogen and the square dots represents the Hoogsteen hydrogen bond.

Based on your attached image, you could use the 3DNA fiber program to build the triplex part, as a starting point. Type fiber -m for available models (especially model #31 (or #30)). That's what the citation you referred to was talking about (as I understand).

See the 3DNA 2003 NAR paper, especially the section titled "MODEL BUILDING". In the 2008 3DNA Nature Protocols paper, pay attention to Box 6:

BOX 6 | FIBER-DIFFRACTION MODELS
The fiber program within 3DNA provides handy access to 55 fiber models of DNA and RNA helices in various polymorphic forms (e.g., A-, B-, C-DNA and so on) and stoichiometries (e.g., single-stranded, double-stranded, triplexes, quadruplexes and DNA–RNA hybrids). The program generates structure files in standard PDB format, with the ‘-xml’ option allowing for structural output in the new Protein Data Bank Markup Language⁷², a format especially useful for very large structures that exceed the five-digit atom serial number limit and/or the fixed (f8.3) Cartesian-coordinate formatting limit of PDB files. To the best of our knowledge, the collection of fiber models in 3DNA is the most comprehensive of its kind. In preparing this set of fiber models, we have taken great care to ensure the accuracy and consistency of the models. For completeness and user verification, 3DNA includes, in addition to 3DNA-processed files, the original coordinates collected from the literature. Whereas the 3DNA-processed repeating unit is necessary to construct full, atomic-level representations of the models, the structurally equivalent PDB files of the repeating units, expressed in standard base reference frame, prove useful as building blocks when a user wishes to generate a perturbed base-only fiber model, such as an overstretched duplex with variable rise at successive steps.

If you want to proceed with 3DNA, please become familiar with the 3DNA fiber command. Of course, you may well want to try some other modeling tools, such as NAB (Nucleic Acid Builder), or the many the start-of-the-art RNA modeling tools, as in the RNA-Puzzles game.

Xiang-Jun