title: Thermodynamics of RNA-RNA binding.
abstract: BACKGROUND
  Reliable prediction of RNA-RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA-mRNA binding and antisense interactions. The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to 'open' the binding site and (2) the energy gained from hybridization.
  
  
  METHODS
  We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired.
  
  
  RESULTS
  Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target.
  
  
  BACKGROUND
  RNAup will be distributed as part of the Vienna RNA Package, www.tbi.univie.ac.at/~ivo/RNA/
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna Währingerstrasse 17, A-1090 Vienna, Austria.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mückstein
authors.forename: Hakim
authors.initials: H
authors.lastname: Tafer
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.forename: Stephan H
authors.initials: SH
authors.lastname: Bernhart
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D008956:Models, Chemical; D015233:Models, Statistical; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000737:chemistry*; D034741:RNA, Small Interfering / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D013816:Thermodynamics
chemical_list: D012333:RNA, Messenger; D034741:RNA, Small Interfering