Scientists say they have visualized, for the first time, fleeting changes in RNA structure that direct biological function through altered cell signalling, and may represent a completely new class of targets for the development of drugs, including those against viral and bacterial pathogens. A team at the University of Michigan’s Department of Chemistry and Biophysics combined an NMR technique with mutagenesis and secondary structural prediction to effectively capture RNA molecules in ‘invisible’ excited states (Es) that last for just milliseconds, but involve changes in localized base-pairing that modify the RNA architecture and cell signalling.

Advances in NMR technology have allowed scientists to characterize rare and transient ‘excited’ protein structures and demonstrate their importance in catalysis, protein folding, signalling, and recognition, but to date, it hasn’t been possible to verify evidence that RNA can also exist in transient excited states. Hashim M. Al-Hashimi, Ph.D., and colleagues now report on the NMR visualization of these RNA ESs on the hexanucleotide apical loop of HIV’s transactivation response element (TAR), HIV-1’s stem loop 1 (SL1, which the studies showed can exist in two different excited states), and the bacterial ribosomal A-site. The results suggest that targeting these ES structures may represent a completely new approach to developing anti-HIV and antibacterial drugs.

More specifically, the team’s findings showed that the TAR ES sequesters four of the apical loop bases into base pairs, essentially preventing them from carrying out binding activities that lead to active transcription of the HIV-1 genome. In essence, they suggest, finding a way to stabilize this transcription-inhibitory excited state may represent a means of targeting TAR in the development of anti-HIV drugs. The two ESs of the HIV-1 SL1, meanwhile, involved base pairs in, above, and below the SL1 internal loop, which appears to impact on the ability SL1 has to form kissing dimmers. And the ES structure of the ribosomal A-site sequesters two adenines into base pairs that makes them unavailable to decode mRNA, and may represent a new way of targeting the A-site for the development of antibiotics.

“These excited states correspond to rare alternative forms that have biological functions,” Dr. Al-Hashimi explains. “These alternative forms have unique architectural and chemical features that could make them great molecules for drugs to latch onto. In some sense they provide a whole new layer of drug targets.”

The University of Michigan team describe their technology and findings in Nature. “Compared to secondary structural transitions observed in many regulatory RNA switches, transitions between the ground and excited states uncovered here involve much more localized changes in RNA structure, occur at rates that are two-to-four orders of magnitude faster, and do not require assistance from external factors,” they write. “Thus, they can meet unique demands in biological circuits and macromolecular machines. The ESs also present new drug targets and offer new opportunities in the engineering of RNA-based devices. Line broadening indicative of ESs is routinely observed in NMR spectra of RNA, and we therefore predict that RNA ESs exist in great abundance throughout the transcriptome.”

Dr. Al-Hashimi and colleagues report their findings in a paper titled “Visualizing transient low-populated structures of RNA.” 

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