The thermodynamics of DNA structural motifs

Annu Rev Biophys Biomol Struct. 2004;33:415-40. doi: 10.1146/annurev.biophys.32.110601.141800.


DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Algorithms
  • Base Pairing
  • DNA / chemistry*
  • DNA Probes / chemistry*
  • Databases, Factual*
  • Models, Chemical*
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Thermodynamics


  • DNA Probes
  • DNA