HIV, the causative agent of AIDS, is a virus that packages two copies of its RNA genetic material into each virus particle. To select this RNA from the many RNAs that are present in the infected cell, part of the viral RNA genome has to fold up into a complex ‘knot’ whose three dimensional structure is distinctive such that it is recognised specifically and the genomic RNA encapsidated. This structure is known as the RNA packaging signal. There have been a large number of published studies on the two dimensional nature of this structure but until now only small regions of it have been solved in three dimensions because of the limitations of techniques such as NMR in solving large RNAs. Here, in collaboration with the Department of Chemistry, we have studied the whole 240 nucleotide packaging signal region.
Using single molecule FRET we have measured the distances between various parts of the RNA structure in solution. Using these distances imposed on the secondary structure model, followed by a comprehensive series of repetitive in silico annealing procedures based on the known geometry of RNA, we have generated for the first time a three dimensional model of this structure. This is the largest viral RNA 3D structure solved under physiological conditions. Apart from revealing the topology of the RNA we find that the structure is consistent with the functional requirements of the packaging signal region. We have also identified previously unpredicted ‘kink-turn’ motifs in the packaging signal which are likely to be protein binding sites. The structure provides the basis for ongoing work investigating its functional domains and also for the design of molecules which will interfere with its function with the aim of generating a novel class of therapeutic drug to use against the virus.
Space filling model of the HIV RNA packaging signal structure
