build a DNA triangle for Gromacs

[glx55483]

Dear Dr. Lu,

I would like to use 3DNA to construct a DNA triangle (as shown in the attached picture) .
In the 3DNA software, can we manually input the coordinates of the central point of each DNA double helix so that they are placed in a specific position? If not, how can the double helix be translated to a specific placement? Also, can such a triangular structure be realized in 3DNA?

Thanks in advance.
Luxuan Guo

[xiangjun]

Hi Luxuan,

Thanks for your interested in using 3DNA and for posting your questions on the 3DNA Forum. Is your DNA triangle a planar structure? Is it equilateral? What the length of each side? Are the three sides connected?

There may be tools (e.g., "AMBER NAB") that better fit your needs. 3DNA does not provide a command to directly construct such a DNA triangle. Nevertheless, 3DNA has some low-level facilities for applications like this. For examples, you could use the fiber command to build three straight helices (in B-or A-form DNA) of selected sequence. Using analyze, you can locate the positions of a regular helix. Combined with case-specific geometric operations, 3DNA may help lead to a bottom-up approach that is reproducible via a script.

Check "build dna bulges and extend dna duplex at both terminals via 3dna" and search the Forum for more applications.

Xiang-Jun