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iPhone app shows 2D structures of thousands of RNA molecules

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Soon scientists will be able to enter a specific RNA from baker's yeast into their iPhone and see a depiction of its two-dimensional structure thanks to a new technology developed at Stanford.

The technology behind the application makes it possible, for the first time, to experimentally capture a global snapshot of the conformation of thousands of RNA molecules in a cell. Previously, the only way to know what shape a particular RNA molecule preferred was to conduct a laborious series of experiments focused on just that molecule.

The research will be published Sept. 2 in Nature and the iPhone app will be available for download on Sept. 15. In a release, senior co-author Howard Chang, MD, PhD explained how the new technology, which powers the iPhone app and a searchable website, will benefit scientists:

It's now possible to look at RNA structure much more quickly and comprehensively. Now we can see patterns that were not previously evident, and begin to categorize RNAs by structure rather than sequence...

...There's so much more information to be discovered. This is just a snapshot of RNAs in isolation. But we can leverage this information for biological insight into how RNA structures may change under different conditions. There are levels of complexity that we're only just beginning to understand.

Since developing the technology, researchers have already identified some surprising patterns. They have learned that regions of RNA that encode specific instructions for protein tend to have more secondary structure than do other regions, and that it is possible to identify the beginning, middle and end of an RNA transcript simply by analyzing its structure. Another key finding was that RNA molecules that had similar functions often have similar structures-perhaps to better direct them to specific locations within the cell.

Baker's yeast was selected to test the technique because it is a well-studied organism with a relatively limited number of RNA molecules in action at any one time-about 3,000 vs. 10,000 in humans. But researchers intend to tackle other organisms soon, and to expand their analysis to include regulatory RNAs that don't carry protein-building instructions.

Photo by Howard Y. Chang

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