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Questions and answers => General discussions (Q&As) => Topic started by: glx55483 on April 17, 2018, 10:06:25 am

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Title: build a DNA triangle for Gromacs
Post by: glx55483 on April 17, 2018, 10:06:25 am
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
Title: Re: build a DNA triangle for Gromacs
Post by: xiangjun on April 17, 2018, 11:43:22 pm
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 (http://casegroup.rutgers.edu/casegr-sh-2.2.html)") 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 (http://forum.x3dna.org/users-contributions/build-dna-bulges-and-extend-dna-duplex-at-both-terminals-via-3dna/)" and search the Forum for more applications.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.