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Questions and answers > RNA structures (DSSR)

Stacking parameters

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spoblete:
Greetings.

I would like to know more specifically the parameters used in the base-stacking classification. I have seen that some almost-perpendicular pairs of bases are annotated as stacked, so I would like to know if the criteria is based uniquely on the hull overlap or if they belong to a more specific perpendicular stacking interaction set.

Many thanks in advance.

Simón.

xiangjun:
Hi Simón,

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

You've touched a subtle, technical point. In DSSR, stacking is decided by no-zero overlapping area of (extended) base-rings projected on the mean plane of the two base normals. The two bases may be (nearly) parallel and stack well, or they are offset, and at a big angle. So being 'stacked' are not equal, as reflected by the different overlap areas and the angles. Users can filter the DSSR-derived stacks based on these two parameters.

These are just general comments. If you provide some specific examples, we can discuss in more detail.

Best regards,

Xiang-Jun

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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.