Does 3DNA work for RNA?

At the C2B2 party this afternoon, I was asked the question: "Does 3DNA work for RNA?" Well, a good question, indeed. The short answer is definitely, YES. However, a detailed explanation is needed to address the underlying intuitive assumption: 3DNA is only for DNA.

1. The name 3DNA was due to Dr. Olson, after we struggled quite a while. Initially, we played with NuStar (which was actually cited once by Richard Dickerson et al), and Carnival etc. I still remember the day when Dr. Olson asked me "How about 3DNA?" We immediately reached an agreement: that's it -- what a cute name! Another advantage (as it becomes clear later): since 3DNA starts with '3', it (mostly) shows up right at the top of many on-line lists of bioinformatics tools.
2. Interpreted literally, 3DNA could mean 3-DNA, i.e., the three most common types of DNA: A-, B- and Z-form. That may be one of the reasons where the misconception that 3DNA is only for 3DNA comes from. Another reason could be that structural work on DNA is what the Olson lab best known for.
   
3. The number '3' in 3DNA should also be associated with its three key components: analysis, rebuilding and visualization. In a sense, this is my favorite.
4. Of course, 3DNA stands for 3D-NA, 3-Dimensional Nucleic Acids, as expressed explicitly in the titles of our two 3DNA papers (2003 NAR and 2008 NP).
   

The applications of 3DNA to RNA structures can be broadly categorized as follows:

1. Automatically detect all existing base-pairs, Watson-Crick (A-U, G-C, wobble G-U) or non-canonical, using a set of simple geometric criteria. Furthermore, it has a unique base-pair classification system based on the six numerical structural parameters, suitable for database storage and search.
   
2. Automatically detect all triplets or higher-order base-associations.
   
3. Automatically detect double helical regions, regardless of backbone connection, thus ideal for finding pseudo-continuous coaxial stacking.
4. The above three features are seamlessly integrated with the visualization component to allow for easy generation of publication quality images. See the 3DNA 2008 NP paper for detailed examples.

As further examples, the following two RNA publications take advantage of find_pair from 3DNA:

• R. Tyagi & D. H. Mathews (2007). Predicting Helical Coaxial Stacking in RNA Multibranch Loops. RNA. 13: 939 - 951. See the note from the authors' webpage for clarification of mis-citation to find_pair.
• R. Capriotti & M. A. Marti-Renom (2009). SARA: a Server for Function Annotation of RNA Structures.
  

It is well worth noting that the base-pair detecting algorithm in RNAView is based on an earlier version of find_pair, a basic fact ignored in the RNAView publication.

In summary, 3DNA works for RNA as well as for DNA, and more.