The thermodynamics of RNA-RNA interaction consists of
two components: the energy necessary to make a potential binding region
accessible, i.e., unpaired, and the energy gained from the base pairing of
the two interaction partners. We show here that both components can
be efficiently computed using an improved variant of RNAup. The method
is then applied to a set of bacterial small RNAs involved in translational
control. In all cases of biologically active sRNA target interactions, the
target sites predicted by RNAup is in perfect agreement with literature.
In addition to prediction of target site location, RNAup can be also be
used to determine the mode of sRNA action. Using information about
target site location and the accessibility change resulting form sRNA
binding we can discriminate between positive and negative regulators of
translation.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:32007 |
| Date | 24 October 2018 |
| Creators | Mückstein, Ulrike, Tafer, Hakim, Bernhart, Stephan H., Hernandez-Rosales, Maribel, Vogel, Jörg, Stadler, Peter F., Hofacker, Ivo L. |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, doc-type:conferenceObject, info:eu-repo/semantics/conferenceObject, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | 978-3-540-70598-7 |
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