SECONDARY STRUCTURE OF THE 3'-NONCODING REGION OF FLAVIVIRUS GENOMES - COMPARATIVE-ANALYSIS OF BASE-PAIRING PROBABILITIES

The prediction of the complete matrix of base pairing probabilities wa s applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary structure element s, but also regions of high structural flexibility. Flaviviruses, many of which are important human pathogens, have a common genomic organiz ation, but exhibit a significant degree of RNA sequence diversity in t he functionally important 3'-NCR. We demonstrate the presence of secon dary structures shared by all flaviviruses, as well as structural feat ures that are characteristic for groups of viruses within the genus re flecting the established classification scheme. The significance of mo st of the predicted structures is corroborated by compensatory mutatio ns. The availability of infectious clones for several flaviviruses wil l allow the assessment of these structural elements in processes of th e viral life cycle, such as replication and assembly.