All eight genes of the original isolate of wild type A/AA/6/60 influenza virus and of the cold adapted A/AA/6/60 vaccine virus have been cloned, sequenced and subjected to RNAfold analysis. Both viruses are ts and attenuated for ferrets. To complete the study, a wild type of the same virus which is both non-ts and virulent will be sequenced and subjected to RNAfold analysis. Relevance of the RNAfolds to the phenotypes of temperature sensitivity and cold adaption as well as to transport of vRNA out of the nucleus will be explored. The second objective of this series of studies is to compare computer generated RNAfold predictions to experimentally deduced structures. SJCRH has a database of 92 nonstructural gene sequences (the smallest gene - 890 bases - of the influenza virus). I propose to study their predicted RNAfolds using the Zuker algorithm on the Y-MP to determine whether the folds of the NS gene will fall into groups corresponding to host of origin and whether conserved domains necessary for functions such as exodus from the cell nucleus may be identified. I will then compare the computer predicted folds to experimentally deduced structures using mung bean nuclease and psoralen cross-linking studies.
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