Problem in 3D structure building of ss DNA aptamer

[Anonymous]

Dear Sir,
Hello!. I am Irshad Baig, pursuing PhD in Biochemistry.

I am writing you to seek your help regarding 3D structure prediction of ss DNA and ssDNA-Protein docking studies.

Infact, I am trying to build 3D model structure for my ss DNA aptamer, as i am further interested to study DNA -protein interaction through docking. However I did not succeed in building 3D struture for ss DNA aptamer.

Trying one reccommended programme,i could able to built 3 D model for ss DNA,however it is in the ‘B’ form of DNA,however i need 3 D model of ss DNA in the native stem/loop form. Further, I have predicted secondary structures of my ssDNA aptamers by Mfold programme, however I did not find any modeling programme to predict tertiary (3D) structure of a DNA, thus would generate PDB/PDBQT file of the DNA aptamers that would be further helpful to study DNA-Protein docking, i assume.

Therefore, I would highly appreciate, if you could please extend me your valuable guidance/suggestions to perform 3D structure prediction of ss DNA aptamer and ss DNA aptamer-Protein docking.

Should you need any information, please do let me know.

Looking forward for your kind reply in this regard.

Thank you,

Sincerely,
Irshad Baig

[Anonymous]

We really don’t have anyone in the Rosetta development community who is working on DNA aptamer structure prediction. The closest we come is the Rhiju Das lab from Stanford, who work with RNA structural prediction. (You can read their papers to see the approaches they use.) So one of the limitations you’ll run into is that there probably won’t be a canned protocol to apply to your system. You’ll have to take some of the RNA structural prediction code and re-purpose it for DNA prediction. (So you may want to look into PyRosetta, which may make doing so easier.) Additionally, there hasn’t been any benchmarking of the energy function for DNA structural prediction, so there may be limitations and caveats to the results you get out. You’ll likely want to assemble a set of examples of known, well characterized structures, and see how well your adjusted protocol does on them before you use it on your experimental system.

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