’Kissing’ RNA and HIV-1: Unraveling the details

A subtle structural change that may play a role in the molecular machinery for making HIV-1 (the virus that causes AIDS) has been identified by scientists from the National Institute of Standards and Technology (NIST) and University of Maryland working at the Center for Advanced Research in Biotechnology (CARB). If confirmed in living cells, the mechanism, described in the Jan. 20 online edition of Proceedings of the National Academy of Sciences, might provide a new target for antiviral drugs.

The finding is among several to emerge recently from CARB’s efforts to develop and validate sensitive tools for rapidly detecting and quantifying ribonucleic acid (RNA) interactions. RNA provides the genetic blueprint for retroviruses such as HIV-1. CARB scientists created a model system for tracking changes in an RNA structural element involved in forming HIV-1 viral particles.

As new HIV-1 viruses form and mature into infectious particles, two strands of RNA interact through a transient structure called a “molecular kiss.” This structure is then packaged into new virus particles, which undergo further maturation after release from the infected cell. CARB scientists found that specific sites in the “kissing” structure acquire a proton (a positively charged particle) at a pH close to that of living cells. The proton’s presence alters the RNA structure and accelerates its refolding by a protein associated with viral maturation. Taken together, these observations suggest that such a mechanism might be at work during viral infection.

To track RNA binding and folding in real-time, the CARB scientists developed fluorescent markers as substitutes for pieces of the RNA. By monitoring changes in the fluorescent signal, the scientists could follow these reactions. The scientists also used nuclear magnetic resonance to identify the sites in the RNA that acquire the proton and to characterize the resulting conformational changes.