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General discussions (Q&As) / Re: How to view triplex DNA with designed sequence via X3DNA?

« on: March 18, 2018, 08:23:12 am »

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?

   

2

General discussions (Q&As) / How to view triplex DNA with designed sequence via X3DNA?

« on: March 15, 2018, 10:10:04 am »

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.