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RNA structures (DSSR) / Concatenated Helices
« on: August 29, 2016, 11:57:54 am »
Hello,

I have been using DSSR to analyze DNA nanocubes containing 12 helices (connected by 3bp single strands to make three-way junctions at the corners of the cube). The cube is initially recognized correctly by DSSR, but after the cube is subjected to molecular dynamics for some time and those results are input, DSSR results show some helices being concatenated for unspecified reasons. Could you please explain the criteria DSSR uses to determine that helices should be concatenated? I have attached part of two output files showing two separate helices at the beginning of MD, and those same helices combined into one helix after 50 nanoseconds.

Thanks in advance.

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.