Thermodynamics of RNA-RNA binding

Bioinformatics. 2006 May 15;22(10):1177-82. doi: 10.1093/bioinformatics/btl024. Epub 2006 Jan 29.


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.

Availability: RNAup will be distributed as part of the Vienna RNA Package,

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Binding Sites
  • Computer Simulation
  • Models, Chemical*
  • Models, Statistical
  • Molecular Sequence Data
  • RNA, Messenger / chemistry*
  • RNA, Small Interfering / chemistry*
  • Sequence Alignment / methods*
  • Sequence Analysis, RNA / methods*
  • Thermodynamics


  • RNA, Messenger
  • RNA, Small Interfering