The Thermodynamics of DNA Structural Motifs
Top Cited Papers
- 9 June 2004
- journal article
- review article
- Published by Annual Reviews in Annual Review of Biophysics and Biophysical Chemistry
- Vol. 33 (1), 415-440
- https://doi.org/10.1146/annurev.biophys.32.110601.141800
Abstract
▪ 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.Keywords
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