Fast switch: RNA vs NMR

New drug targets

 

Researchers have used NMR spectroscopy to tease out details of the smallest and fastest-known molecular switches composed of ribonucleic acid, RNA. These structures exist only fleetingly (lasting just 45-250 microseconds) and in low abundance (2–13%) yet look set to be become important targets for the development of new antiviral and antibiotic drugs.

Biophysical chemist Hashim Al-Hashimi of the University of Michigan and colleagues Elizabeth Dethoff, Katja Petzold, Jeetender Chugh and Anette Casiano-Negroni have revealed once again that RNA, previously thought only to function as a data storage medium for DNA information transfer actually performs many other tasks all while morphing between various structural forms.

It is known that DNA is used to make RNA molecules in our cells and RNA, of course, plays a crucial role in the regulation of gene expression. Moreover, increasing numbers of clues about how RNA directs the actors on the cellular stage have emerged in recent years. These macromolecules act as switches that are able to detect cellular signals and then to respond by changing their own form to propagate the appropriate information to other biomolecules within the cell. In molecular biology function follows form in many regards. Al-Hashimi and his team were well aware of this switching role in RNA.

Writing in the journal Nature this month, the team has revealed a new class of RNA switches that are much smaller than their more well known cellular counterparts. Moreover, these molecular switches flip states several orders of magnitude more quickly than those counterparts into an excited state form as revealed by NMR spectroscopy, hinting at functionality of which chemists are not yet aware.

"We're finally able to zoom in on these rare, alternative forms of RNA that exist for just a split second and then are gone," explains Al-Hashimi discussing what his team have dubbed RNA micro-switches. "These things are so difficult to see because they exist for roughly 1 percent of the time and for only a microsecond to a millisecond." Al-Hashimi points out that the excited states his team have found correspond to rare alternative forms that have unique architectural and chemical features that would make excellent targets for small molecule drugs. "In some sense, they provide a whole new layer of drug targets," he says.

The team investigated transient structural changes in three types of RNA molecules: two from HIV, which are known to play an important role in the replication of the AIDS virus. The third is, they say, involved in the biochemical quality control takes place within the cellular protein factory, the ribosome, and so represents an important target for interfering with bacterial replication for instance or in aspects of protein quality control in diseases in which the machinery of the ribosome goes awry in our own cells.

Accumulating evidence

The researchers suggests that indirect evidence has been accumulating for the existence of RNA micro-switches for many years, but this work represents perhaps the first direct view. Moreover, their NMR technique in which the trapped RNA structures are analysed can also be used to generate a "video-like sequence showing how RNA molecules change shape, twisting, bending and rotating about their structural joints.

"The next steps are to broadly explore the occurrence of these RNA micro-switches in the transcriptome, more deeply explore their biological functions, and apply strategies for drug discovery that involve trapping these transient form in either their "on" or 'off' states," Al-Hashimi told SpectroscopyNOW. "To enable these goals, we are developing approaches for predicting these alternative structures based on RNA sequence and methods for determining their structure at very high atomic resolution."