Messages

1

RNA structures (DSSR) / Re: Concatenated Helices

« on: August 31, 2016, 11:00:02 am »

Hi,

Thank you for your prompt response. Here are the PDB files as mentioned. I have attached the files for the minimized structure (MIN), the structure after 50 nanoseconds of MD, and after 100 nanoseconds of MD. Please let me know of any findings.

Thanks again,
Katie

2

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.