DNA Crossing

[jabbasaccount]

Hello,

I am relatively new to the software. I am trying to make a .pdb file for a nucleic acid structure that is made up of multiple components and I am having trouble finding any information on how to approach the problem.

In particular, I am trying to build a structure that contains a crossing of two dna double-helices where I need to be able to decide which single-strands of the double helices connect.

Can I maybe have a pointer where to look or some helpful examples?

Thank you for your time,
Jasper

[xiangjun]

Hi Jasper,

I think I sort of understand what you mean. You could use 'fiber' or 'rebuild' to build a regular double helix, and then manually break it at the point of interest in one strand.

As always, a concrete example would make your point clear.

Xiang-Jun

[jabbasaccount]

Thank you very much for the quick response.

I am trying to build variations of the tensegrity triangle, generated by changing the strand connections in the three corners.

The .pdb file of the the tensegrity triangle as found on rcsb.org uses the asymmetric units to create the triangle. However, I would like to generate .pdb files describing the different corners obtained when connecting the strands in different ways. Afterwards, I would like to combine the different corners to form triangles.

Here is the link to the rcsb.org page for the tensegrity triangle for reference:
http://www.rcsb.org/pdb/explore/explore.do?structureId=4B8D

Thank you once again for your time,
Jasper

[xiangjun]

Thanks for the link to PDB entry 4b8d. As far as I can tell, it won't be straightforward with 3DNA to generate .pdb files for the corners to form triangles. That said, if you have such a pdb file for the corners to begin with, you may use 'mutate_bases' to change bases as desired. Alternatively, you may find NAB from AmberTools helpful.

Xiang-Jun

[jabbasaccount]

I will have a closer look at it in the course of the next few weeks. If i find a solution using 3dna or if i have further questions i will report back here.

Thanks for the great support.

[xiangjun]

Please let me know how it goes. Wherever practical, I am willing to improve 3DNA to facilitate the process. 3DNA stays relevant by building on concrete, real-world examples.

Xiang-Jun