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Stanford researchers make first direct observation of 3-D molecule folding in real time
Date:2/14/2008

o the RNA. To do this, they tack a long strand of DNA on one side.

Under the microscope, the two plastic beads look like tiny pearls against a gray backdrop. The researchers pull the beads apart, taking into account two factors: force and extension. By understanding how much force it takes to cause a certain amount of extension of the RNA, they can describe with unsurpassed accuracy how the folds form and the energy needed to make each fold happen.

"When you pull it apart, different structures will pop open-pop, pop, pop-and you can see the order in which different structural elements get pulled apart," Block said. "You can map out the order in which the pieces come together, for both folding and unfolding."

Learning by force

To build a clear picture of how their riboswitch folded in real time, the researchers mapped out the energy of the molecule's folding based on the forces required to uncurl it and the time the RNA took to re-curl. Block calls the energy graph the "crown jewel of the work," adding that "all the numbers you'd like to know about this folding sequence are right in front of you in that diagram."

Block's team could only attain this detailed "energy landscape" of the RNA's folding by physically toying with the molecule. The particular RNA they studied folds four times, and each time it adopts a more stable, more comfortable configuration with lower energy. If it grabs an adenine, it hangs on tightly because it is in its most stable state. But because molecules are always jiggling, sometimes a fold pops open briefly. The more stable each fold is, the less likely it is to come undone. The researchers stretched out the RNA to study all four folded states, noting how stable each one was.

Using force, Block's team described not only the energy of each fold in the RNA, but the energy it needed to go from one folded state to the next, and how often the folds popped open and closed in real time. The
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Contact: Louis Bergeron
louisb3@stanford.edu
650-725-1944
Stanford University
Source:Eurekalert

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