"Nanovideo” Captures Motion of RNA Molecules in 3D

Using an innovative variation on the traditional solution state nuclear magnetic resonance (NMR) spectroscopy technique, investigators have produced a "nanovideo” that reveals in three dimensions how RNA molecules change shape--information that may prove useful in developing drugs against viruses such as HIV.

Similar animations have been produced from theoretic calculations, but video, developed by Dr. Hashim Al-Hashimi, from the University of Michigan (U-M; Ann Arbor, MI, USA), is based on actual experimental data and covers a much longer timescale than the simulations.

Once believed to simply store and relay genetic information, RNA now is known to perform a range of other functions, from regulating gene expression and other vital cellular processes to serving as a sensor that detects cellular signals and performs appropriate reactions in response. The versatile molecule also is essential to viruses such as HIV, which have no DNA and instead rely on RNA to both carry and execute genetic instructions for everything the virus needs to invade and overwhelm its host.

Typically, RNA works by binding to something else and then radically changing shape. The shape alterations, in turn, trigger other processes, or cascades of events. Scientists know about the shifting shapes because they have seen before-and-after images of RNA, first in its unbound state, then when it is bound to something. The static images distinctly show that the molecule assumes different conformations, but they do not reveal how it changes from one shape to another.

Dr. Al-Hashimi's new nanovideo offers a three-dimensional (3D) view at how parts of the molecule--which has ladder-like arms connected by a flexible hub or linker--twist, bend, and rotate relative to one another. Obtaining such information through traditional NMR is impossible, according to Dr. Al-Hashimi, because the technique measures motion relative to the magnetic field in which the sample is placed. That frame of reference can capture motion only from one point of view, resulting in a one-dimensional measurement. To obtain a 3D view that reveals how parts of the molecule move relative to one another, Dr. Al-Hashimi's group devised with a strategy that would allow them to position the magnetic field first on the molecule's upper arm and then on its lower arm.

"Moving the frame of reference onto the molecule and measuring the same motion from different points of view is like taking pictures from different angles,” said Dr. Al-Hashimi, an assistant professor of chemistry and an assistant research scientist in the U-M biophysics research division. "We sit on one arm and watch the other moving; then we sit on the other arm and watch the first arm moving. By combining the measurements, we come up with a 3D view.”

The data revealed that the two arms simultaneously twist and bend and that their motion is not random but very coordinated, exposing a new level of organization in how molecules change shapes. The nanovideo Dr. Al-Hashimi's group produced from the data also provides a longer look at molecular motions than do animations based on theoretic calculations. While those animations show motion that occurs over only one nanosecond (one billionth of a second), the movie spans approximately one millisecond (one thousandth of a second).

Understanding the details of RNA motion can be helpful in designing drugs that interact with viral RNA. If researchers know which parts are likely to change to accommodate a drug and which parts are likely to remain rigid, they can more precisely target drugs to interact with the molecule. In the research, Dr. Al-Hashimi's team evaluated a specific RNA molecule from HIV known as TAR, which is critical for viral replication and thus is a key target for anti-HIV drugs.

The technique used in this work also should be applicable other types of biologically and medically important molecules, such as proteins, according to Dr. Al-Hashimi.

The research was reported in the December 20, 2008, issue of the journal Nature.


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