JILA study of RNA dynamics may help in drug design

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JILA study of RNA dynamics may help in drug design

15 Jul 2005 Medical News Today

Biophysicists have developed a method for studying, in real time, a

nanoscale " docking and undocking " interaction between small pieces of

ribonucleic acid (RNA), a technique that may be broadly useful in

studying structural changes in RNA that affect its function. The

research at JILA, a joint institute of the National Institute of

Standards and Technology (NIST) and University of Colorado at

Boulder, may have applications in the design of effective new drugs

based on small RNA strands.

RNA is a chain-like molecule that contains genetic information, makes

proteins and catalyzes biological reactions. Scientists at JILA are

studying RNA using methods that reveal how individual chemical units

of RNA dock, or lightly and temporarily bond, to form special three-

dimensional shapes that exhibit biochemical activity. The latest

work, to be published the week of July 11 in the Proceedings of the

National Academy of Sciences,* adds to understanding of the

intramolecular " stickiness " between specific loops and sequences in

the RNA that help stabilize this folding. This type of information is

crucial to understanding RNA structure and, ultimately, how it

affects function.

The JILA group developed a simple model system for studying the

reversible docking of a small piece of RNA at a receptor site in the

same molecule. They used a technique called fluorescence resonance

energy transfer, in which the two pieces of RNA are labeled with

different dyes that have overlapping emission bands. One dye emits

light of the same color that the other dye absorbs; the second dye

then emits light of a different color. One piece of RNA is excited by

a laser and, when the two pieces are close enough together to dock,

passes energy to the other one, which then fluoresces. This method

was used to measure the distance between the two pieces of RNA as it

varied from less than 4 nanometers in the docked state to about 7 nm

in the undocked state.

The scientists used ultrasensitive laser-based microscopy methods to

image many isolated RNA molecules simultaneously, in effect

generating a " movie " of single molecule docking kinetics in real

time. They used this method to study thousands of pieces of RNA over

time scales of 10 to 30 seconds, and observed about two-thirds of

them rapidly docking and undocking. The rates of docking and

undocking were measured as a function of the concentration of

magnesium ions in the surrounding fluid, revealing a complex

dependence on metal ions, as is typical for RNA. The docking rate

rose 12-fold as magnesium concentrations increased. A significant

number of molecules still docked in the absence of magnesium--the

first time this phenomenon has been observed, according to the paper.

The research is supported by NIST, the National Science Foundation,

National Institutes of Health, and the W.M. Keck Foundation

initiative in RNA science at CU-Boulder.

*J.H. Hodak, J.L. Fiore, D.J. Nesbitt, C.D. Downey and A. Pardi.

2005. Docking kinetics and equilibrium of a GAAA tetraloop-receptor

motif probed by single molecule fluorescence resonance energy

transfer. Proceedings of the National Academy of Sciences. Week of

July 11.

National Institute of Standards and Technology (NIST)

http://www.nist.gov