I want to simulate hairpin DNA with drug complex, but I found it difficult to design pdb file for hairpin DNA. I tried few available online resources but can not design, the sequence I am using is known to form hairpin structure in aqueous solution, any suggestion will be appreciated.
Thanks in advance
You can do it using Avogadro. First you need to model the stem region. Then, make a single strand of the loop region. Then, connect the two 5'--3' ends, thus, attaching the loop to the stem. Then freeze the atoms of the stem and do a geometry optimisation. In Avogadro, the optimisation process is interactive, therefore, you can perturb the orientation of bases in the loop region by dragging atoms.
Thanks Uttam for reply,
Can you please provide link to follow your suggestions, or can you make it more clear to find "stem" and connecting "loops". I tried following your suggestions, still the 3d structure is incomplete.. any suggestions ?
An experimental, atomic-resolution structure of a hairpin DNA available in the Protein Data Bank (PDB) can be used as a template for re-building using X3DNA.
Note: If you know the structure, you know the intra- and inter-base-pair geometrical parameters, and vice versa.
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PDB: http://www.rcsb.org/pdb/home/home.do
X3DNA: http://x3dna.org/
i highly suggest this tool
http://unafold.rna.albany.edu/?=mfold
you can also follow this pipeline
https://www.nature.com/articles/s41598-017-01348-5#Sec2
I found out that using Avagadro will be helpful, but when we make pdb and psf file for MD, it was observed that the bonds designed in Avagadro were have some problems.
I used another approach,
1. convert your DNA sequence to RNA sequence,
2. Get the RNA haripin secondary structure from here (http://www.nupack.org/), and then use the squence + secondary structure information here (http://rnacomposer.cs.put.poznan.pl/),
3. Now you will obtain a pdb file, edit it using Coot (http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/) or use PyMol for few atom, here you can mutate whole residue from U to T.
4. Then its done, in NAMD the psf and pdb can be generated using Amber ff.
Hi Abhishek,
Can you teach how to generate the psf file manually? I had problem when running AutoPSF of my file, as attached;
Dear Sabri,
Send me your structure file (pdb), i need to check it, did you used parametrized structure
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