Concatenated Helices

[dapkuskm]

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.

[xiangjun]

Hi,

Thanks for using DSSR, and for posting your questions on the 3DNA Forum.

The basic definition of helix/stem in DSSR is quite simple, as shown in Fig. 1E of the NAR paper (see below). However, the implementation is non-trivial (with some empirical settings) to account for numerous boundary cases in real-world structures.

The DSSR default settings for identifying helices/stems work well, from my experience. However, the results may not be "intuitive" for certain situations, like yours. Your MD simulation trajectories change over time, and after 50 ns, two previously separated helices may become close together to be combined. This is not surprising. However, to get to the bottom of how/why this concatenation happens, I need to have sample PDB files. The PDB coordinate files do not need to be "real", if you are sensitive to your unpublished data, as long as they can help reproduce the reported problem.

Best regards,

Xiang-Jun

[dapkuskm]

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

[xiangjun]

Hi Katie,

Thanks for attaching three of your MD structures -- the minimized one looks amazing!

I've visualized the three structures in Jmol, and noticed quite significant distortions in the 50ns and 100ns structures. DSSR is performing as designed, even though the results are not what you expected. When a structure is distorted, the boundary between different helices are no longer clear. DSSR uses a geometric approach to identify stacking regions of base pairs. Using your 50ns structure as an example, helix#5 is a concatenation of two helices because of the stacking of DA240 on the DG95--DC242 pair. On the other hand, some DSSR-derived helices in 50ns are quite short. Overall, if you can visualize a fragment as helix-like in Jmol/PyMOL, DSSR should be able to find it.

Are the 12 helices a requirement during your MD simulations? Your 50ns and 100ns structures show that some pairs are broken or formed in the process. Moreover, the single-stranded connecting regions are not always 3 nucleotides.

Xiang-Jun