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Titel:
Secondary Structure of the 3'-Non-Coding Region of Flavivirus
Genomes Comparative Analysis of Base Pairing Probabilities
Author(s):
Susanne Rauscher,
Christoph Flamm,
Christian W. Mandl,
Franz X. Heinz,
Peter F. Stadler
Appeared in:
RNA, 3, 779-791 (1997)
Abstract:
The prediction of the complete matrix of base pairing probabilities
was applied to the 3' non-coding region (NCR) of flavivirus genomes. This
approach identifies not only well-defined secondary structure elements
but also regions of high structural flexibility. Flaviviruses, many of
which are important human pathogens, have a common genomic organisation
but exhibit a significant degree of RNA sequence diversity in the functionally
important 3'-NCR. We demonstrate the presence of secondary structures
shared by all flaviviruses as well as structural features that are
characteristic for groups of viruses within the genus reflecting the
established classification scheme. The significance of most of the
predicted structures is corroborated by compensatory mutations. The
availability of infectious clones for several flaviviruses will allow
to assess the involvement of these structures in specific processes of
the viral life cycle, such as replication and assembly.
Keywords:
RNA secondary structure,
structural alignment,
base pairing probabilities,
flavivirus,
3'-noncoding region
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