100
views
0
recommends
+1 Recommend
0 collections
    4
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      The thermodynamics of DNA structural motifs.

      Read this article at

      ScienceOpenPublisherPubMed
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          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.

          Related collections

          Author and article information

          Journal
          Annu Rev Biophys Biomol Struct
          Annual review of biophysics and biomolecular structure
          Annual Reviews
          1056-8700
          1056-8700
          2004
          : 33
          Affiliations
          [1 ] Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA. jsl@chem.wayne.edu
          Article
          10.1146/annurev.biophys.32.110601.141800
          15139820
          619b64bd-eadc-4b4a-b446-5053a82f663e
          History

          Comments

          Comment on this article