Dissection of the interactions involved in replication of foot and mouth disease virus using RNA aptamers

Foot-and-mouth disease virus was the cause of a recent major disease outbreak in the UK that resulted in the slaughter of 4,000,000 animals and financial losses estimated to have approached 30 billion pounds. It remains endemic in many parts of the world and it is clear that further outbreaks of the disease will occur in the UK. The disease is caused by a virus and in order to effectively fight such infections in the future, we need to increase our knowledge of how this disease agent functions and find out what makes it different from the cells it invades. Viruses are composed of one or more pieces of nucleic acid (DNA or RNA) enclosed in a protective coat. The simplest coats are made of protein. During an infection, viruses turn their host's cells into factories for the production of new virus particles, however, these can only be viable if the viral nucleic acid is reproduced accurately in the infected cell. This process is therefore a potential 'Achilles-heel' in the viral life-cycle. This project aims to help us understand how the nucleic acid molecules of foot-and-mouth disease virus are recognised by proteins of the replication machinery by producing molecules that specifically bind to these proteins. These molecules, called aptamers, can either 'mimic' the normal binding sites of the proteins, or can bind elsewhere. Both types of aptamers could affect the action of the replication proteins, helping us understand how the replication process occurs and possibly determine target sites for the design of antiviral drugs in the future.

We propose to employ RNA aptamers to define the binding site of the RNA-dependant RNA polymerase of foot-and-mouth disease virus (FMDV) and to dissect important contacts involved in recognition and to extend these studies to investigate other proteins in the replication complex. Preliminary studies have resulted in RNA aptamers that specifically recognise and inhibit the activity of FMDV RNA-dependant RNA polymerase in vitro, with IC50 values of 11-22 nM. One of these molecules has been truncated to a 32 mer that retains its affinity and inhibitory capability. Preliminary co-crystallisation studies have shown density corresponding to the RNA. We now propose to define the minimal fragment necessary for polymerase binding in order to define the RNA-protein contacts involved. This information will then be used for a mutagenesis programme in order to dissect the details of the recognition event. Studies will be extended to include other components of the replicase complex and to investigate aptamer specificity with respect to different serotypes of the virus.